Microdevices and biosensor cartridges for biological or chemical analysis and systems and methods for the same

ABSTRACT

A flow cell including inlet and outlet ports in fluid communication with each other through a flow channel that extends therebetween. The flow channel includes a diffuser region and a field region that is located downstream from the diffuser region. The field region of the flow channel directs fluid along reaction sites where desired reactions occur. The fluid flows through the diffuser region in a first flow direction and through the field region in a second flow direction. The first and second flow directions being substantially perpendicular.

CROSS REFERENCE TO RELATED APPLICATION

The present application is a continuation of U.S. application Ser. No.14/729,809 (“the '809 Application”), filed Jun. 3, 2015, now U.S. Pat.No. 9,387,476, which is a continuation of U.S. application Ser. No.13/882,088 (“the '088 Application”), filed Apr. 26, 2013, now U.S. Pat.No. 9,096,899, which is a National Stage of International ApplicationNo. PCT/US2011/057111, filed Oct. 20, 2011, which claims the benefit ofU.S. Provisional Application Ser. No. 61/407,350 (“the '350Application”), filed Oct. 27, 2010. Each of the '809 Application, the'088 Application, and the '350 Application is incorporated herein byreference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under NIH Grant NumberHG003571 awarded by the PHS. The Government has certain rights in theinvention.

BACKGROUND OF THE INVENTION

Embodiments of the present invention relate generally to biological orchemical analysis and more particularly, to systems and methods usingmicrofluidic and detection devices for biological or chemical analysis.

Various protocols in biological or chemical research involve performinga large number of controlled reactions on local support surfaces orwithin predefined reaction chambers. The desired reactions may then beobserved or detected, and subsequent analysis may help identify orreveal properties of chemicals involved in the reaction. For example, insome multiplex assays, an unknown analyte having an identifiable label(e.g., fluorescent label) may be exposed to thousands of known probesunder controlled conditions. Each known probe may be deposited into acorresponding well of a microplate. Observing any chemical reactionsthat occur between the known probes and the unknown analyte within thewells may help identify or reveal properties of the analyte. Otherexamples of such protocols include known DNA sequencing processes, suchas sequencing-by-synthesis or cyclic-array sequencing. In cyclic-arraysequencing, a dense array of DNA features (e.g., template nucleic acids)are sequenced through iterative cycles of enzymatic manipulation. Aftereach cycle, an image may be captured and subsequently analyzed withother images to determine a sequence of the DNA features.

As a more specific example, one known DNA sequencing system uses apyrosequencing process and includes a chip having a fused fiber-opticfaceplate with millions of wells. A single capture bead having clonallyamplified sstDNA from a genome of interest is deposited into each well.After the capture beads are deposited into the wells, nucleotides aresequentially added to the wells by flowing a solution containing aspecific nucleotide along the faceplate. The environment within thewells is such that if a nucleotide flowing through a particular wellcomplements the DNA strand on the corresponding capture bead, thenucleotide is added to the DNA strand. Incorporation of the nucleotideinto the DNA strand initiates a process that ultimately generates achemiluminescent light signal. The system includes a CCD camera that ispositioned directly adjacent to the faceplate and is configured todetect the light signals from the wells. Subsequent analysis of theimages taken throughout the pyrosequencing process can determine asequence of the genome of interest.

However, the above pyrosequencing system, in addition to other systems,may have certain limitations. For example, the fiber-optic faceplate isacid-etched to make millions of small wells. Although the wells may beapproximately spaced apart from each other, it is difficult to know aprecise location of a well in relation to other adjacent wells. When theCCD camera is positioned directly adjacent to the faceplate, the wellsare not evenly distributed along the pixels of the CCD camera and, assuch, the wells are not aligned in a known manner with the pixels.Inter-well crosstalk between the adjacent wells makes distinguishingtrue light signals from the well of interest from other unwanted lightsignals difficult in the subsequent analysis. As a result, data recordedduring the sequencing cycles must be carefully analyzed. Furthermore,the above system uses a high-resolution camera (16 Megapixels) todetermine true signals from unwanted crosstalk. However, thehigh-resolution camera generates large amounts of data that must beanalyzed that, in turn, may slow down the process. The high-resolutioncamera can also be expensive.

Furthermore, the above pyrosequencing system may use a number ofenzymatic strategies to reduce crosstalk. For example, the system mayuse apyrase to degrade unincorporated nucleotide species and ATP,exonuclease to degrade linear nucleic acid molecules, pyrophosphatase(also referred to as PPi-ase) to degrades PPi, and/or enzymes to inhibitactivity of other enzymes. However, these enzymatic strategies mayincrease the total costs of sequencing and may also negatively affectthe system's ability to discern the true light signals for a certainwell.

Moreover, sequencing systems and other bioassay systems must fluidiclydeliver reagents and enzymes to the wells or other reaction sites andremove the unused reagents and enzymes. Some challenges that arise indelivering/removing the reagents and enzymes include bubble formationwithin a fluidic system. Bubbles disrupt the flow of the fluids throughthe faceplate as well as negatively affect the imaging of a reactionsites. Furthermore, if a system does not have uniform flow through thefaceplate, then some wells may not be properly washed or may receive thereagents at different times or in different concentrations with respectto other wells in the chip. This may lead to misleading or incorrectdata.

Bioassay systems are also typically configured to perform only one assayprotocol or very similar protocols. For example, the CCD camera in thepyrosequencing system described above may have unique features and beconfigured to detect light signals emitted from the wells of thefaceplate. However, the features and predetermined configuration of theCCD camera may not be suitable for other types of sequencing protocolsor other assay protocols. As such, the system may be limited to onlythose protocols that require the CCD camera to be predisposed in asimilar way.

In addition to the above challenges and limitations, there is a generalneed for more user-friendly bioassay systems that reduce costs relativeto other known systems and also increase control and efficiency of thereactions intended to be observed.

BRIEF DESCRIPTION OF THE INVENTION

In accordance with one embodiment, a biosensor cartridge configured toengage a bioassay system is provided. The biosensor cartridge includes aflow cell having inlet and outlet ports and a flow channel that extendstherebetween. The flow cell can include a substrate field comprising aplurality of reaction chambers. The reaction chambers have aperturesthat open onto the flow channel such that the reaction chambers are influid communication with the flow channel. The biosensor cartridge canalso include an activity detector that is coupled to the flow cell andhas an array of pixels that have a fixed positioned relative to thesubstrate field. The pixels may be assigned to select reaction chamberssuch that activity detected by the pixels indicates that a desiredreaction has occurred within the select reaction chamber. The biosensorcartridge also includes an exterior side surface that has a plurality ofelectrical contacts thereon that are communicatively coupled to thepixels. The electrical contacts of the side surface are configured toengage corresponding mating contacts of a bioassay system.

In another embodiment, a biosensor cartridge that is configured toremovably engage a bioassay system is provided. The biosensor cartridgeincludes a flow cell having inlet and outlet ports and a flow channelthat extends therebetween. The biosensor cartridge also includes anactivity detector that is coupled to the flow cell and is configured todetect activity along the flow channel that is indicative of desiredreactions. The biosensor cartridge may also have first and second sidesurfaces. The first side surface can include the inlet and outlet ports.The second side surface can include electrical contacts that arecommunicatively coupled to the activity detector. The first and secondside surfaces may face in substantially opposite directions.

In yet another embodiment, a flow cell is provided that includes inletand outlet ports in fluid communication with each other through a flowchannel that extends therebetween. The flow channel has a diffuserregion and a field region that is located downstream from the diffuserregion. The field region of the flow channel directs fluid alongreaction sites where desired reactions occur. The fluid flows throughthe diffuser region in a first flow direction and through the fieldregion in a second flow direction. The first and second flow directionscan be substantially perpendicular to each other.

In a further embodiment, a workstation for biological or chemicalanalysis is provided. The workstation includes a receptacle that isconfigured to receive and establish electrical and fluidic couplingswith a microdevice and a fluidic control system for controlling a flowof fluid through the microdevice. The fluidic control system includes anupstream conduit for delivering the fluid and a downstream conduit forremoving the fluid. The workstation also includes a user interface thatis configured to receive user selections or inputs and a systemcontroller that includes an identification module and a protocol module.The identification module is configured to receive signals relating toidentification information of the microdevice. The protocol module isconfigured to determine at least one parameter of an assay protocolbased at least in part on the identification information. An operationof the fluidic control system is based at least in part on thedetermined at least one parameter.

In another embodiment, a system receptacle that is configured to engagea biosensor cartridge is provided. The system receptacle includes analignment assembly that is configured to hold the biosensor cartridge ina predetermined orientation. The system receptacle also includes anupstream conduit for delivering fluid to the biosensor cartridge and adownstream conduit for removing the fluid from the biosensor cartridge.The upstream and downstream conduits include respective nozzles. Thesystem receptacle also includes an actuation device that is configuredto move the nozzles of the upstream and downstream conduits toward thebiosensor cartridge in an axial direction to establish a fluidicconnection.

In a further embodiment, a workstation for biological or chemicalanalysis is provided. The workstation includes a workstation housing anda fluidic-control system at least partially positioned within thehousing. The fluidic-control system includes an upstream conduit fordelivering fluid to a biosensor cartridge and a downstream conduit forremoving the fluid from the biosensor cartridge. The system receptacleis configured to receive the biosensor cartridge. The system receptacleincludes an alignment assembly that is configured to hold the biosensorcartridge in a predetermined orientation and upstream and downstreamnozzles fluidicly coupled to the upstream and downstream conduits,respectively. The system receptacle also includes an actuation devicethat is configured to move the nozzles of the upstream and downstreamconduits toward the alignment assembly in an axial direction toestablish a fluidic connection with the biosensor cartridge.

In yet another embodiment, a reservoir bag is provided that has top andbottom ends and a height extending therebetween. A gravitational forcedirection is configured to extend from the top end to the bottom endwhen the reservoir bag is in operation. The reservoir bag includes atleast one flexible wall that defines a variable volume for holding afluid. The volume has a main storage portion, a flow path portion, and abridge portion. The main storage portion and the flow path portion arein fluid communication with each other through the bridge portion. Thereservoir bag also includes a bag opening that is located proximate tothe top end. The fluid flowing through the bag opening when the fluid isremoved. The reservoir bag also includes a partition that projects fromthe top end toward the bottom end to a distal tip and separates the mainstorage and flow path portions. The bridge portion is located betweenthe distal tip and the bottom end.

In one embodiment, a bioassay system is provided that is configured toengage a microdevice for performing desired reactions and detectingactivity that is indicative of the desired reactions. The bioassaysystem includes a system receptacle configured to engage the microdeviceand a fluidic-control system that is configured to control a flow offluid through the microdevice. The fluidic-control system is in fluidcommunication with the microdevice. The bioassay system also includes afluid storage system that is fluidicly coupled to the fluidic-controlsystem. The fluid storage system is configured to provide reagents to beused for the desired reactions within the microdevice. The bioassaysystem also includes a temperature control system and a user interfacethat is configured to receive user inputs from a user of the bioassaysystem. Furthermore, the bioassay system includes a system controllerthat is configured to control operation of the fluidic-control, thefluid storage, and the temperature control systems. The systemcontroller is also configured to receive the user inputs from the userinterface. The user inputs may relate to an assay protocol to run whenthe microdevice is engaged. The system controller may also communicatedetection data to the user interface. The user interface can display thedetection data to the user.

In another embodiment, a method of manufacturing a biosensor cartridgeis provided. The method comprises providing a base substrate includingan activity detector that has an array of pixels and circuitry forcommunicating data regarding activity detected by the pixels. The basesubstrate has an exterior side surface that includes a plurality ofelectrical contacts thereon that are communicatively coupled to thepixels through the circuitry. The method also includes mounting asubstrate layer over the array of pixels. The substrate layer caninclude a plurality of reaction chambers where desired reactions areconducted. The substrate layer is mounted over the array of pixels suchthat the pixels are assigned to select reaction chambers. Activitydetected by the assigned pixels indicates that a desired reaction hasoccurred within the select reaction chamber.

In yet another embodiment, a method of conducting an assay protocolusing directed condensation is provided. The method includes providing aflow cell that has a flow channel and a substrate layer having aplurality of reaction chambers therein that are in fluid communicationwith the flow channel. The flow cell includes a cover wall that isspaced apart from the substrate layer. The cover wall separates the flowchannel and an exterior side surface. The flow channel directs a flow offluid between the cover wall and the substrate layer. The method alsoincludes interfacing a thermal element with an engagement area of theside surface. The thermal element is configured to transfer or absorbthermal energy of the fluid in the flow channel through the cover wall.The method also includes providing thermal energy to the fluid withinthe flow channel during an assay protocol. The thermal energy isabsorbed by the fluid within the flow channel and transferred to thefluid within the reaction chambers.

In another embodiment, a method of amplifying and sequencing DNA withina flow cell is provided. The method includes providing a flow cell thathas a flow channel and a substrate layer having a plurality of reactionchambers therein that are in fluid communication with the flow channel.The flow cell includes a cover wall that is spaced apart from thesubstrate layer and defines the flow channel therebetween. The flowchannel directs a flow of fluid between the cover wall and the substratelayer. The reaction chambers include DNA samples therein. The methodalso includes flowing a first aqueous solution that includes at leastone of reagents and enzymes for DNA amplification through the flowchannel. The method also includes flowing a non-polar liquid through theflow channel such that the first aqueous solution is substantiallyremoved from the flow channel. The reaction chambers include the firstaqueous solution therein that interfaces with the non-polar liquid inthe flow channel. The method also includes controlling a temperature ofthe first aqueous solution in the reaction chambers to perform DNAamplification and flowing a second aqueous solution through the flowchannel to remove the first aqueous solution. Furthermore, the methodincludes flowing a third aqueous solution through the flow channel thatincludes at least one of reagents and enzymes for DNA sequencing.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a block diagram of a system for biological or chemicalanalysis formed in accordance with one embodiment.

FIG. 2 is a block diagram of a system controller that may be used in thesystem of FIG. 1.

FIG. 3 is a block diagram of a workstation for biological or chemicalanalysis in accordance with one embodiment.

FIG. 4 provides perspective views of the workstation of FIG. 3.

FIG. 5 is a partially exploded perspective view of a biosensor cartridgeformed in accordance with one embodiment.

FIG. 6 shows plan views of the biosensor cartridge of FIG. 5.

FIG. 7 illustrates a cross-section of a microdevice formed in accordancewith one embodiment.

FIG. 8 illustrates a perspective view of a portion of the microdeviceshown in FIG. 7.

FIG. 9 is a plan view of a reaction chamber that may be used with themicrodevice of FIG. 7.

FIG. 10 is a schematic illustration of an exemplary activity detectorformed in accordance with various embodiments.

FIG. 11 is an image of a fiber-optic faceplate that may be used invarious embodiments.

FIG. 12 is a cross-section of the faceplate shown in FIG. 11.

FIG. 13 is a top perspective view of a flow cover that may be used invarious embodiments.

FIG. 14 is a bottom perspective view of the flow cover of FIG. 13.

FIG. 15 is a top perspective view of another flow cover that may be usedin various embodiments.

FIG. 16 is a bottom perspective view of another flow cover that may beused in various embodiments.

FIG. 17 is a top perspective of the flow cover in FIG. 16.

FIG. 18 is a top perspective view of a flow cover formed in accordancewith another embodiment.

FIG. 19 is a top perspective view of a flow cover formed in accordancewith another embodiment.

FIG. 20 illustrates an exemplary embodiment of a planar flow coverformed in accordance with various embodiments.

FIG. 21 is a top view of a biosensor cartridge formed in accordance withone embodiment including the flow cover of FIG. 20.

FIG. 22 is a bottom view of the biosensor cartridge of FIG. 21.

FIG. 23 is a perspective view of a system receptacle formed inaccordance with one embodiment.

FIG. 24 is a bottom perspective view of a mounting assembly of thesystem receptacle of FIG. 23.

FIG. 25 is a perspective view of an alignment assembly that may be usedwith the system receptacle of FIG. 23.

FIG. 26 is a cross-section of the system receptacle in the unengagedposition.

FIG. 27 is a different cross-section of the system receptacle in theengaged position.

FIG. 28 is a partial perspective view of a fluid storage unit formed inaccordance with one embodiment.

FIG. 29 is a top plan view of the storage unit of FIG. 28.

FIG. 30 is a side view of a fluid reservoir bag formed in accordancewith one embodiment.

FIG. 31 is a cross-section of the biosensor cartridge shown in FIG. 5.

DETAILED DESCRIPTION OF THE INVENTION

Embodiments described herein may be used in various biological orchemical processes and systems for academic or commercial analysis. Morespecifically, embodiments described herein may be used in variousprocesses and systems where it is desired to detect an event, property,quality, or characteristic that is indicative of a desired reaction. Forexample, embodiments described herein include biosensor cartridges,microdevices, and their components as well as bioassay systems thatoperate with the biosensor cartridges and microdevices. In particularembodiments, the biosensor cartridges and microdevices include a flowcell and an activity detector that are coupled together in asubstantially unitary structure.

The bioassay systems may be configured to perform a plurality of desiredreactions that may be detected individually or collectively. Themicrodevices and bioassay systems may be configured to perform numerouscycles where the plurality of desired reactions occur in parallel. Forexample, the bioassay systems may be used to sequence a dense array ofDNA features through iterative cycles of enzymatic manipulation andimage acquisition. As such, the biosensor cartridges and microdevicesmay include one or more microfluidic channels that deliver reagents orother reaction components to a reaction site. In some embodiments, thereaction sites are reaction chambers that compartmentalize the desiredreactions therein. Furthermore, embodiments may include an activitydetector that is configured to detect activity that is indicative of thedesired reactions.

As used herein, a “desired reaction” includes a change in at least oneof a chemical, electrical, physical, and optical property or quality ofa substance that is in response to a stimulus. For example, the desiredreaction may be a chemical transformation, chemical change, or chemicalinteraction. The desired reaction may also be a change in electricalproperties. For example, the desired reaction may be a change in ionconcentration within a solution. Exemplary reactions include, but arenot limited to, chemical reactions such as reduction, oxidation,addition, elimination, rearrangement, esterification, amidation,etherification, cyclization, or substitution; binding interactions inwhich a first chemical binds to a second chemical; dissociationreactions in which two or more chemicals detach from each other;fluorescence; luminescence; chemiluminescence; and biological reactions,such as nucleic acid replication, nucleic acid amplification, nucleicacid hybridization, nucleic acid ligation, phosphorylation, enzymaticcatalysis, receptor binding, or ligand binding. The desired reaction canalso be addition or elimination of a proton, for example, detectable asa change in pH of a surrounding solution or environment.

The stimulus can be at least one of physical, optical, electrical,magnetic, and chemical. For example, the stimulus may be an excitationlight that excites fluorophores in a substance. The stimulus may also bea change in a surrounding environment, such as a change in concentrationof certain biomolecules (e.g., enzymes or ions) in a solution. Thestimulus may also be an electrical current applied to a solution withina predefined volume. In addition, the stimulus may be provided byshaking, vibrating, or moving a reaction chamber where the substance islocated to create a force (e.g., centripetal force). As used herein, thephrase “in response to a stimulus” is intended to be interpreted broadlyand include more direct responses to a stimulus (e.g., when afluorophore emits energy of a specific wavelength after absorbingincident excitation light) and more indirect responses to a stimulus inthat the stimulus initiates a chain of events that eventually results inthe response (e.g., incorporation of a base in pyrosequencing eventuallyresulting in chemiluminescence). The stimulus may be immediate (e.g.,excitation light incident upon a fluorophore) or gradual (e.g., changein temperature of the surrounding environment).

As used herein, the phrase “activity that is indicative of a desiredreaction” and grammatical variants thereof include any detectable event,property, quality, or characteristic that may be used to facilitatedetermining whether a desired reaction has occurred. For example, thedetected activity may be a light signal generated in fluorescence orchemiluminescence. The detected activity may also be a change inelectrical properties of a solution within a predefined volume or alonga predefined area. The detected activity may be a change in temperature.

As used herein, a “reaction component” or “reactant” includes anysubstance that may be used to obtain a desired reaction. For example,reaction components include reagents, enzymes, samples, otherbiomolecules, and buffer solutions. The reaction components aretypically delivered to a reaction site in a solution or immobilizedwithin a reaction site. The reaction components may interact directly orindirectly with the substance of interest.

As used herein, the term “reaction site” is a localized region where adesired reaction may occur. A reaction site may include support surfacesof a substrate where a substance may be immobilized thereon. Forexample, a reaction site may include a substantially planar surface in achannel of a flow cell that has a colony of clonally amplified sstDNAthereon. Furthermore, a plurality of reactions sites may be arrangedside-by-side in a matrix, such as in microarrays. A reaction site canalso include a reaction chamber that at least partially defines aspatial region or volume configured to compartmentalize the desiredreaction. As used herein, the term “reaction chamber” includes a spatialregion that is in fluid communication with a flow channel. The reactionchamber may be at least partially separated from the surroundingenvironment or other spatial regions. For example, a plurality ofreaction chambers may be separated from each other by shared walls. As amore specific example, the reaction chamber may include a cavity definedby interior surfaces of a well and have an opening or aperture so thatthe cavity may be in fluid communication with a flow channel.

In some embodiments, the reaction chambers are sized and shaped relativeto solids (including semi-solids) so that the solids may be inserted,fully or partially, therein. For example, the reaction chamber may besized and shaped to accommodate only one capture bead. The capture beadmay have clonally amplified DNA or other substances thereon.Alternatively, the reaction chamber may be sized and shaped to receivean approximate number of beads or solid substrates. As another example,the reaction chambers may also be filled with a porous gel or substancethat is configured to control diffusion or filter fluids that may flowinto the reaction chamber.

As used herein, a “substance” includes items or solids, such as capturebeads, as well as biological or chemical substances. As used herein, a“biological or chemical substance” includes biomolecules, samples ofinterest, and other chemical compound(s). A biological or chemicalsubstance may be used to detect, identify, or analyze other chemicalcompound(s), or function as intermediaries to study or analyze otherchemical compound(s). In particular embodiments, the biological orchemical substances include a biomolecule. As used herein, a“biomolecule” includes at least one of nucleosides, nucleic acids,polynucleotides, oligonucleotides, proteins, enzymes, polypeptides,antibodies, antigens, ligands, receptors, polysaccharide, carbohydrate,polyphosphates cells, tissues, organisms, and any other biologicallyactive chemical compound(s) such as analogs or mimetics of theaforementioned species.

In a further example, a biological or chemical substance or abiomolecule includes an enzyme or reagent used in a coupled reaction todetect the product of another reaction such as an enzyme or reagent usedto detect pyrophosphate in a pyrosequencing reaction. Enzymes andreagents useful for pyrophosphate detection are described, for example,in U.S. Patent Publication No. 2005/0244870 A1, which is incorporatedherein in its entirety.

Biomolecules, samples, and biological or chemical substances may benaturally occurring or synthetic and may be suspended in a solution ormixture within a spatial region. Biomolecules, samples, and biologicalor chemical substances may also include a pharmaceutical composition. Insome cases, biomolecules, samples, and biological or chemical substancesof interest may be referred to as targets, probes, or analytes.

As used herein, a “microdevice” and a “biosensor cartridge” include astructure having a plurality of the reaction sites. A microdevice or abiosensor cartridge may include at least one of a flow channel and anelectrical circuit. For example, a microdevice or a biosensor cartridgemay include at least one flow channel that is in fluid communicationwith the reaction sites. As such, the microdevice or biosensor cartridgemay be referred to as a microfluidic device. In some embodiments, thebiosensor cartridge includes a microdevice. For example, after themicrodevice is prepared or manufactured, the microdevice may be coupledto a housing or container to form the biosensor cartridge. In someembodiments, the microdevices and the biosensor cartridges may beself-contained, disposable units. However, other embodiments may includean assembly with removable parts that allow a user to access an interiorof the microdevice for maintenance or replacement of components orsamples. The microdevice and the biosensor cartridge may be removablycoupled or engaged to larger bioassay systems, such as a sequencingsystem, that conducts controlled reactions therein.

In particular embodiments, the microdevice or biosensor cartridge mayinclude an activity detector. As used herein, an “activity detector” isany device or component that is capable of detecting the activity thatis indicative of a desired reaction. An activity detector may be abledetect predetermined events, properties, qualities, or characteristicswithin a predefined volume or area. For example, an activity detectormay be able to capture an image of the predefined volume or area. Anactivity detector may be able detect an ion concentration within apredefined volume of a solution or along a predefined area. Exemplaryactivity detectors include charged-coupled devices (CCD's) (e.g., CCDcameras); photomultiplier tubes (PMI's); molecular characterizationdevices or detectors, such as those used with nanopores; microcircuitarrangements, such as those described in U.S. Pat. No. 7,595,883, whichis incorporated herein by reference in the entirety; and CMOS-fabricatedsensors having field effect transistors (FET's), including chemicallysensitive field effect transistors (chemFET), ion-sensitive field effecttransistors (ISFET), and/or metal oxide semiconductor field effecttransistors (MOSFET).

However, in other embodiments, the microdevice or biosensor cartridgedoes not include the activity detector. Such microdevices or biosensorcartridges may include flow cells that are configured to be positionedadjacent to an activity detector. For example, the microdevice may be aflow cell that is positioned directly adjacent to a CCD camera.

As used herein, when the terms “removably” and “coupled” (or “engaged”)are used together to describe a relationship between the microdevice (orbiosensor cartridge) and a system receptacle or interface of a bioassaysystem, the term is intended to mean that a connection between themicrodevice and the system receptacle is readily separable withoutdestroying the system receptacle. Accordingly, the microdevice may beremovably coupled or engaged to the system receptacle in an electricalmanner such that the mating contacts of the bioassay system are notdestroyed. The microdevice may be removably coupled or engaged to thesystem receptacle in a mechanical manner such that the features thathold the microdevice are not destroyed. The microdevice may be removablycoupled or engaged to the system receptacle in a fluidic manner suchthat the ports of the system receptacle are not destroyed. The systemreceptacle or a component is not considered to be “destroyed,” forexample, if only a simple adjustment to the component (e.g., realigning)or a simple replacement (e.g., replacing a nozzle) is required. However,in other embodiments where noted, the microdevice and the systemreceptacle may be readily separable without destroying either themicrodevice or the system receptacle. Components are readily separablewhen the components may be separated from each other without undueeffort or a significant amount of time spent in separating thecomponents.

As used herein, the term “fluid communication” or “fluidicly coupled”refers to two spatial regions being connected together such that aliquid or gas may flow between the two spatial regions. For example, amicrofluidic channel may be in fluid communication with a reactionchamber such that a fluid may flow freely into the reaction chamber fromthe microfluidic channel. The terms “in fluid communication” or“fluidicly coupled” allow for two spatial regions being in fluidcommunication through one or more valves, restrictors, or other fluidiccomponents that are configured to control or regulate a flow of fluidthrough a system. In some cases, two spatial regions may be in fluidcommunication with each other even if, under certain conditions, acertain fluid would not be able to flow freely into a spatial region.For example, although a reaction chamber may be in fluid communicationwith a flow channel if the fluid were an aqueous solution, the interiorsurfaces of the reaction chamber may be modified or have certainproperties that prevent the fluid from flowing into the reaction chamberwhen the fluid is a non-polar solution. For instance, the fluid may beoil and the interior surfaces of the reaction chamber may behydrophilic.

As used herein, the term “immobilized,” when used with respect to abiomolecule or biological or chemical substance, includes substantiallyattaching the biomolecule or biological or chemical substance at amolecular level to a surface. For example, biomolecule or biological orchemical substance may be immobilized to a surface of the substratematerial using adsorption techniques including non-covalent interactions(e.g., electrostatic forces, van der Waals, and dehydration ofhydrophobic interfaces) and covalent binding techniques where functionalgroups or linkers facilitate attaching the biomolecules to the surface.Immobilizing biomolecules or biological or chemical substances to asurface of a substrate material may be based upon the properties of thesubstrate surface, the liquid medium carrying the biomolecule orbiological or chemical substance, and the properties of the biomoleculesor biological or chemical substances themselves. In some cases, asubstrate surface may be first modified to have functional groups boundto the surface. The functional groups may then bind to biomolecules orbiological or chemical substances to immobilize them thereon.

In some embodiments, nucleic acids can be attached to a surface andamplified using bridge amplification. Useful bridge amplificationmethods are described, for example, in U.S. Pat. No. 5,641,658; U.S.Patent Publ. No. 2002/0055100 A1; U.S. Pat. No. 7,115,400; U.S. PatentPubl. No. 2004/0096853 A1; U.S. Patent Publ. No. 2004/0002090 A1; U.S.Patent Publ. No. 2007/0128624 A1; and U.S. Patent Publ. No. 2008/0009420A1, each of which is incorporated herein in its entirety. Another usefulmethod for amplifying nucleic acids on a surface is rolling circleamplification (RCA), for example, using methods set forth in furtherdetail below.

In particular embodiments, the assay protocols executed by the systemsand methods described herein include the use of natural nucleotides andalso enzymes that are configured to interact with the naturalnucleotides. Natural nucleotides include, for example, ribonucleotidesor deoxyribonucleotides. Natural nucleotides can be in the mono-, di-,or tri-phosphate form and can have a base selected from adenine (A),Thymine (T), uracil (U), guanine (G) or cytosine (C). It will beunderstood however that non-natural nucleotides or analogs of theaforementioned nucleotides can be used. Some examples of usefulnon-natural nucleotides are set forth below in regard to reversibleterminator-based sequencing by synthesis methods.

In some embodiments, items or solid substances (including semi-solidsubstances) may be disposed within the reaction chambers. When disposed,the item or solid may be physically held or immobilized within thereaction chamber through an interference fit, adhesion, or entrapment.Exemplary items or solids that may be disposed within the reactionchambers include polymer beads, pellets, agarose gel, powders, quantumdots, or other solids that may be compressed and/or held within thereaction chamber. In particular embodiments, a nucleic acidsuperstructure, such as a DNA ball, can be disposed in or at a reactionchamber, for example, by attachment to an interior surface of thereaction chamber or by residence in a liquid within the reactionchamber. A DNA ball or other nucleic acid superstructure can bepreformed and then disposed in or at the reaction chamber.Alternatively, a DNA ball can be synthesized at the reaction chamber. ADNA ball can be synthesized by rolling circle amplification to produce aconcatamer of a particular nucleic acid sequence and the concatamer canbe treated with conditions that form a relatively compact ball. DNAballs and methods for their synthesis are described, for example in,U.S. Patent Publ. Nos. 2008/0242560 A1 or 2008/0234136 A1, each of whichis incorporated herein in its entirety.

A substance that is held or disposed in a reaction chamber can be in asolid, liquid, or gaseous state. A substance can be held in a reactionchamber in the same state that it was introduced to the reactionchamber. For example, a liquid substance can be loaded into a reactionchamber and the substance can remain liquid whether or not it isconverted to a different chemical species. Alternatively, a substancecan be introduced to a reaction chamber in a first state and thenconverted to another state.

As used herein, an “environment” may be liquid, gas, or solid or acombination thereof. The environments in the reaction chambers and theflow channel may be different. As used herein, when the terms “separate”or “isolate” are used with respect to a surrounding environment and asubstance within a reaction chamber, the substance may be separate fromthe surrounding environment without being completely isolated from thesurrounding environment. For instance, a fluid in the flow channel mayinterface with, but not substantially intermix with through diffusionand the like, the environment or substance in the reaction chamber. Byway of a more specific example, a hydrophilic solution within thereaction chamber may interface with a non-polar liquid that flowsthrough the flow channel. In alternative embodiments, separation of asubstance from a surrounding environment can be a fluidic isolation suchthat the substance in the reaction chamber is prevented from makingphysical contact with the surrounding environment. For example, areaction chamber may be capped or sealed.

The reaction chambers and flow channels may have microfluidic dimensionsin which surface tension and cohesive forces of a liquid in the reactionchamber and the adhesive forces between the liquid and interior surfacesthat define the reaction chamber can have a significant effect on theliquid therein. As understood by those skilled in the art, a liquid mayhave different wetting abilities to a solid surface depending upon thenatures of the liquid and the solid surface. Wetting is a liquid'sability to spread along a solid surface. The wetting of a solid surfaceby a liquid is controlled by the intermolecular interactions ofmolecules along an interface between the two phases. If the adhesiveforces are relatively greater than the cohesive forces, the wetting ofthe liquid to the surface is greater. If the cohesive forces arerelatively greater than the adhesive forces, the wetting of the liquidto the surface is smaller. Embodiments may utilize the wetting abilitiesof a fluid during the course of an assay or other usage.

In embodiments utilizing aqueous or polar liquids, the interactionbetween the liquid and the solid surface can be characterized ashydrophobic or hydrophilic. As used herein, a solid surface ishydrophobic if it repels an aqueous or polar liquid. For example, acontact angle between the aqueous or polar liquid and the hydrophobicsurface of the solid is typically greater than 90 degrees. A surface ishydrophilic if it is attracted to an aqueous or polar liquid. Forexample, a contact angle between the aqueous or polar liquid and thehydrophilic surface of the solid will typically be less than 90 degrees.

In other embodiments, a non-polar liquid, such as alkanes, oils, andfats, may be used as the liquid within the reaction chamber and/or aspart of the surrounding environment. Non-polar liquids may be attractedto a surface that has a hydrophobic interaction with aqueous or polarliquids. Likewise, non-polar liquids are not attracted to a surface thathas a hydrophilic interaction with aqueous or polar liquids. As such,hydrophobic and hydrophilic surfaces may be used with embodimentsdescribed herein to control the flow of liquids through portions of theflow channel or within the reaction chambers.

Other factors may affect the contact angle or the wetting of a liquid toa solid. For example, a purity of the liquid or whether a surfactant isused may affect the surface tension of the liquid and the molecularinteractions along the solid-liquid interface. A purity of the solid orwhether a coating is placed on the solid surface may affect the surfaceenergy of a solid. Also, temperature of the environment, a compositionof the surrounding air, and the roughness or smoothness of the surfacemay all affect the interactions between the liquid and the solidsurface. As such, embodiments described herein may utilize these otherfactors for certain purposes.

FIG. 1 is a block diagram of a bioassay system 100 for biological orchemical analysis formed in accordance with one embodiment. The term“bioassay” is not intended to be limiting as the bioassay system 100 mayoperate to obtain any information or data that relates to at least oneof a biological and chemical substance. In some embodiments, thebioassay system 100 is a workstation that may be similar to a bench-topdevice or desktop computer. For example, a majority of the systems andcomponents for conducting the desired reactions can be within a commonhousing 116.

In particular embodiments, the bioassay system 100 is a nucleic acidsequencing system (or sequencer) configured for various applications,including de novo sequencing, resequencing of whole genomes or targetgenomic regions, and metagenomics. The sequencer may also be used forRNA analysis. By way of example, the bioassay system 100 may read, forexample, 100,000 beads and at about a 400 bp read length. Furthermore,in some embodiments, the bioassay system 100 may amplify templatenucleic acid before sequencing of the nucleic acid is initiated.

The bioassay system 100 is configured to interact with a microdevice (orbiosensor cartridge) 102 to perform desired reactions within themicrodevice 102. In particular embodiments, the bioassay system 100 isconfigured to perform massively parallel reactions within themicrodevice 102. The microdevice 102 includes one or more reaction siteswhere desired reactions can occur. The reaction sites can be, forexample, elongated channels, reaction chambers, or planar surfaces. Themicrodevice 102 includes a flow channel that receives fluid from thebioassay system 100 and directs the fluid toward the reaction sites.Optionally, the microdevice 102 is configured to engage a thermalelement for transferring thermal energy into or out of the flow channel.Furthermore, in some embodiments, the microdevice 102 includes anactivity detector for detecting activity that is indicative of theoccurrence of one or more desired reactions.

The bioassay system 100 may include various components, assemblies, andsystems (or sub-systems) that interact with each other to perform apredetermined method or assay protocol for biological or chemicalanalysis. For example, the bioassay system 100 includes a systemcontroller 104 that may communicate with the various components,assemblies, and sub-systems of the bioassay system 100 and also themicrodevice 102. The bioassay system 100 may also include a systemreceptacle or interface 112 that engages the microdevice 102; a fluidiccontrol system 106 to control the flow of fluid throughout a fluidnetwork of the bioassay system 100 and the microdevice 102; a fluidstorage system 108 that is configured to hold all fluids that may beused by the bioassay system; and a temperature control system 110 thatmay regulate the temperature of the fluid in the fluid network, thefluid storage system 108, and/or the microdevice 102.

Also shown, the bioassay system 100 may include a user interface 114that interacts with the user. For example, the user interface 114 mayinclude a display 113 to display or request information from a user anda user input device 115 to receive user inputs. In some embodiments, thedisplay 113 and the user input device 115 are the same device (e.g.,touchscreen). As will be discussed in greater detail below, the bioassaysystem 100 may communicate with various components to perform thedesired reactions. The bioassay system 100 may also be configured toanalyze the detection data to provide a user with desired information.

The system controller 104 may include any processor-based ormicroprocessor-based system, including systems using microcontrollers,reduced instruction set computers (RISC), application specificintegrated circuits (ASICs), field programmable gate array (FPGAs),logic circuits, and any other circuit or processor capable of executingfunctions described herein. The above examples are exemplary only, andare thus not intended to limit in any way the definition and/or meaningof the term system controller. In the exemplary embodiment, the systemcontroller 104 executes a set of instructions that are stored in one ormore storage elements, memories, or modules in order to at least one ofobtain and analyze detection data. Storage elements may be in the formof information sources or physical memory elements within the bioassaysystem 100.

The set of instructions may include various commands that instruct thebioassay system 100 or microdevice 102 to perform specific operationssuch as the methods and processes of the various embodiments describedherein. The set of instructions may be in the form of a softwareprogram. As used herein, the terms “software” and “firmware” areinterchangeable, and include any computer program stored in memory forexecution by a computer, including RAM memory, ROM memory, EPROM memory,EEPROM memory, and non-volatile RAM (NVRAM) memory. The above memorytypes are exemplary only, and are thus not limiting as to the types ofmemory usable for storage of a computer program.

The software may be in various forms such as system software orapplication software. Further, the software may be in the form of acollection of separate programs, or a program module within a largerprogram or a portion of a program module. The software also may includemodular programming in the form of object-oriented programming. Afterobtaining the detection data, the detection data may be automaticallyprocessed by the bioassay system 100, processed in response to userinputs, or processed in response to a request made by another processingmachine (e.g., a remote request through a communication link).

The system controller 104 may be connected to the microdevice 102 andthe other components of the bioassay system 100 via communication links.The system controller 104 may also be communicatively connected tooff-site systems or servers. The communication links may be hardwired orwireless. The system controller 104 may receive user inputs or commands,from the user interface 114. The user input device 115 may include akeyboard, mouse, a touch-screen panel, and/or a voice recognitionsystem, and the like. Alternatively or in addition, the user inputdevice 115 may also be the display 113.

The fluidic control system 106 includes a fluid network and isconfigured to direct and regulate the flow of one or more fluids throughthe fluid network. The fluid network may be in fluid communication withthe microdevice 102 and the fluid storage system 108. For example,select fluids may be drawn from the fluid storage system 108 anddirected to the microdevice 102 in a controlled manner, or the fluidsmay be drawn from the microdevice 102 and directed toward, for example,a waste reservoir in the fluid storage system 108. Although not shown,the fluidic control system 106 may include flow sensors that detect aflow rate or pressure of the fluids within the fluid network. Thesensors may communicate with the system controller 104.

The temperature control system 110 is configured to regulate thetemperature of fluids at different regions of the fluid network, thefluid storage system 108, and/or the microdevice 102. For example, thetemperature control system 110 may include a thermocycler thatinterfaces with the microdevice 102 and controls the temperature of thefluid that flows along the reaction sites in the microdevice 102. Thetemperature control system 110 may also regulate the temperature ofsolid elements or components of the bioassay system 100 or themicrodevice 102. Although not shown, the temperature control system 110may include sensors to detect the temperature of the fluid or othercomponents. The sensors may communicate with the system controller 104.

The fluid storage system 108 is in fluid communication with themicrodevice 102 and may store various reaction components or reactantsthat are used to conduct the desired reactions therein. The fluidstorage system 108 may also store fluids for washing or cleaning thefluid network and microdevice 102 and for diluting the reactants. Forexample, the fluid storage system 108 may include various reservoirs tostore reagents, enzymes, other biomolecules, buffer solutions, aqueous,and non-polar solutions, and the like. Furthermore, the fluid storagesystem 108 may also include waste reservoirs for receiving wasteproducts from the microdevice 102.

The system receptacle or interface 112 is configured to engage themicrodevice 102 in at least one of a mechanical, electrical, and fluidicmanner. The system receptacle 112 may hold the microdevice 102 in adesired orientation to facilitate the flow of fluid through themicrodevice 102. The system receptacle 112 may also include electricalcontacts that are configured to engage the microdevice 102 so that thebioassay system 100 may communicate with the microdevice 102 and/orprovide power to the microdevice 102. Furthermore, the system receptacle112 may include fluidic ports (e.g., nozzles) that are configured toengage the microdevice 102. In some embodiments, the microdevice 102 isremovably coupled to the system receptacle 112 in a mechanical manner,in an electrical manner, and also in a fluidic manner.

In some embodiments, the bioassay system 100 may have interchangeable orswappable devices (e.g., plug-and-play). For example, the systemreceptacle 112 may be readily replaced or substituted with a differentsystem receptacle. This may occur when a different type of microdevice102 is desired to be used. Furthermore, the fluid storage system 108 maybe a container that is readily separated from the fluid network andreplaced by another container. This may occur when the fluid in thecontainer is depleted, has expired, or a different container is requiredbecause a user of the bioassay system 100 desires to run a differentassay protocol. Furthermore, the system controller 104 may haveswappable devices (e.g., if the user desires to use the bioassay system100 to execute a different assay protocol).

In addition, the bioassay system 100 may communicate remotely with othersystems or networks. Detection data obtained by the bioassay system 100may be stored in a remote database.

FIG. 2 is a block diagram of the system controller 104 in the exemplaryembodiment. In one embodiment, the system controller 104 includes one ormore processors or modules that can communicate with one another. Thesystem controller 104 is illustrated conceptually as a collection ofmodules, but may be implemented utilizing any combination of dedicatedhardware boards, DSPs, processors, etc. Alternatively, the systemcontroller 104 may be implemented utilizing an off-the-shelf PC with asingle processor or multiple processors, with the functional operationsdistributed between the processors. As a further option, the modules ofdescribed below may be implemented utilizing a hybrid configuration inwhich certain modular functions are performed utilizing dedicatedhardware, while the remaining modular functions are performed utilizingan off-the-shelf PC and the like. The modules also may be implemented assoftware modules within a processing unit.

During operation, a communication link 120 may transmit commands to orreceive data from the microdevice 102 (FIG. 1) and/or the sub-systems106, 108, 110 (FIG. 1). A communication link 122 may receive user inputfrom the user interface 114 (FIG. 1) and transmit data or information tothe user interface 114. Data from the microdevice 102 or sub-systems106, 108, 110 may be processed by the system controller 104 in real-timeduring a bioassay session. Additionally or alternatively, data may bestored temporarily in a system memory during a bioassay session andprocessed in less than real-time or off-line operation.

The system controller 104 may include a plurality of modules 131-138that communicate with a main control module 130. The main control module130 may communicate with the user interface 114 (FIG. 1). Although themodules 131-138 are shown as communicating directly with the maincontrol module 130, the modules 131-138 may also communicate directlywith each other, the user interface 114, and the microdevice 102. Also,the modules 131-138 may communicate with the main control module 130through the other modules.

The plurality of modules 131-138 include system modules 131-133 thatcommunicate with the sub-systems 106, 108, and 110, respectively. Thefluidic control module 131 may communicate with the fluidic controlsystem 106 to control the valves and flow sensors of the fluid networkfor controlling the flow of one or more fluids through the fluidnetwork. The fluid storage module 132 may notify the user when fluidsare low or when the waste reservoir must be replaced. The fluid storagemodule 132 may also communicate with the temperature control module 133so that the fluids may be stored at a desired temperature.

The plurality of modules 131-138 may also include a device module 134that communicates with the microdevice 102 and an identification module135 that determines identification information relating to themicrodevice 102. The device module 134 may, for example, communicatewith the system receptacle 112 to confirm that the microdevice hasestablished an electrical and fluidic connection with the bioassaysystem 100. The identification module 135 may receive signals thatidentify the microdevice 102. The identification module 135 may use theidentity of the microdevice 102 to provide other information to theuser. For example, the identification module 135 may determine and thendisplay a lot number, a date of manufacture, or a protocol that isrecommended to be run with the microdevice 102.

The plurality of modules 131-138 may also include a detection dataanalysis module 138 that receives and analyzes the detection data (e.g.,image data) from the microdevice 102. The processed detection data maybe stored for subsequent analysis or may be transmitted to the userinterface 114 to display desired information to the user.

Protocol modules 136 and 137 communicate with the main control module130 to control the operation of the sub-systems 106, 108, and 110 whenconducting predetermined assay protocols. The protocol modules 136 and137 may include sets of instructions for instructing the bioassay system100 to perform specific operations pursuant to predetermined protocols.The protocol modules 136 and 137 include a sequencing-by-synthesis (SBS)module 136 that may be configured to issue various commands forperforming sequencing-by-synthesis processes. In some embodiments, theSBS module 136 may also process detection data.

By way of one example, the SBS module 136 may be configured to issuevarious commands for performing the steps of a pyrosequencing protocol.In this case, the microdevice 102 may include millions of wells whereeach well has a single capture bead having clonally amplified sstDNAthereon. Each well may also include other smaller beads that, forexample, may carry immobilized enzymes (e.g., ATP sulfurylase andluciferase) or facilitate holding the capture bead in the well. The SBSmodule 136 may be configured to issue commands to the fluidic controlmodule 106 to run consecutive cycles of fluids that carry a single typeof nucleotide (e.g., 1st cycle: A; 2nd cycle: G; 3rd cycle: C; 4thcycle: T; 5th cycle: A; 6th cycle: G; 7th cycle: C; 8th cycle: T; andon). When a nucleotide is incorporated into the DNA, pyrophosphate isreleased thereby instigating a chain reaction where a burst of light isgenerated. The burst of light may be detected by an activity detector.Detection data may be communicated to the main control module 130, thedetection data analysis module 138, and/or the SBS module 136 forprocessing. The detection data may be stored for later analysis or maybe analyzed by the system controller 104 and an image may be sent to theuser interface 114.

The SBS module 136 may also be configured to issue commands for othersequencing-by-synthesis processes. For example, the SBS module 136 mayissue commands to perform bridge PCR where clusters of clonal ampliconsare formed on localized areas within a channel (or lane) of a flow cell.After generating the amplicons through bridge PCR, the amplicons may be“linearized” to make sstDNA and a sequencing primer may be hybridized toa universal sequence that flanks a region of interest. For example, areversible terminator-based sequencing by synthesis method can be usedas follows. Each sequencing cycle extends the sstDNA by a single baseand is accomplished by modified DNA polymerase and a mixture of fourtypes of nucleotides. The different types of nucleotides can have uniquefluorescent labels, and each nucleotide can further have a reversibleterminator that allows only a single-base incorporation to occur in eachcycle. After a single base is added to the sstDNA, an image in fourchannels is taken (i.e., one for each fluorescent label). After imaging,the fluorescent label and the terminator are chemically cleaved from thesstDNA. Another similar sequencing cycle may follow. In such asequencing protocol, the SBS module 136 may instruct the fluidic controlsystem 106 to direct a flow of reagent and enzyme solutions through themicrodevice 102. Exemplary reversible terminator-based SBS methods whichcan be utilized with the apparatus and methods set forth herein aredescribed in US Patent Application Publication No. 2007/0166705 A1, USPatent Application Publication No. 2006/0188901 A1, U.S. Pat. No.7,057,026, US Patent Application Publication No. 2006/0240439 A1, USPatent Application Publication No. 2006/0281109 A1, PCT Publication No.WO 05/065814, US Patent Application Publication No. 2005/0100900 A1, PCTPublication No. WO 06/064199 and PCT Publication No. WO 07/010251, eachof which is incorporated herein by reference in its entirety. Exemplaryreagents for reversible terminator-based SBS are described in U.S. Pat.No. 7,541,444; U.S. Pat. No. 7,057,026; U.S. Pat. No. 7,414,116; U.S.Pat. No. 7,427,673; U.S. Pat. No. 7,566,537; U.S. Pat. No. 7,592,435 andWO 07/135368, each of which is incorporated herein by reference in itsentirety.

The plurality of protocol modules may also include an amplificationmodule 137 that is configured to issue commands to the fluidic controlsystem 106 and the temperature control system 110 for amplifying aproduct within the microdevice 102. For example, the microdevice 102 maybe engaged to the bioassay system 100. The bioassay system 100 mayidentify the type of microdevice or other information and automaticallyrun an amplification protocol. Alternatively, the bioassay system 100may request additional information from the user. The amplificationmodule 137 may issue instructions to the fluidic control system 106 todeliver necessary amplification components to reaction chambers withinthe microdevice 102. The reaction chambers may already contain somecomponents for amplification, such as the template DNA and/or primers.After delivering the amplification components to the reaction chambers,the amplification module 137 may instruct the temperature control system110 to cycle through different temperature stages according to knownamplification protocols.

In some embodiments, the amplification and SBS modules may operate in asingle assay protocol where, for example, template nucleic acid isamplified and subsequently sequenced within the same biosensorcartridge.

In some embodiments, the user may provide user inputs through the userinterface 114 to select an assay protocol to be run by the bioassaysystem 100. In other embodiments, the bioassay system 100 mayautomatically detect the type of microdevice 102 that has been insertedinto the system receptacle 112 and confirm with the user the assayprotocol to be run. Alternatively, the bioassay system 100 may offer alimited number of assay protocols that could be run with the determinedtype of microdevice 102. The user may select the desired assay protocol,and the bioassay system 100 may then perform the selected assay protocolbased on preprogrammed instructions.

However, the bioassay system 100 may also allow the user to reconfigurean assay protocol. After determining the assay protocol to run, thebioassay system 100 may offer options to the user through the userinterface 114 for modifying the determined protocol. For example, if itis determined that the microdevice 102 is to be used for amplification,the bioassay system 100 may request a temperature for the annealingcycle. Furthermore, the bioassay system 100 may issue warnings to a userif a user has provided user inputs that are generally not acceptable forthe selected assay protocol.

FIG. 3 is a block diagram of an exemplary workstation 200 for biologicalor chemical analysis in accordance with one embodiment. The workstation200 may have similar features, systems, and assemblies as the bioassaysystem 100 described above. For example, the workstation 200 may have afluidic control system, such as the fluidic control system 106 (FIG. 1),that is fluidicly coupled to a biosensor cartridge or microdevice 235through a fluid network 238. The fluid network 238 may include a reagentcartridge 240, a valve block 242, a main pump 244, a debubbler 246, a3-way valve 248, a flow restrictor 250, a waste removal system 252, anda purge pump 254. In particular embodiments, most of the components orall of the components describe above are within a common workstationhousing 230 (FIG. 4).

A flow of fluid is indicated by arrows along the fluid network 238. Forexample, reagent solutions may be removed from the reagent cartridge 240and flow through the valve block 242. The valve block 242 may facilitatecreating a zero-dead volume of the fluid flowing to the biosensorcartridge 235 from the reagent cartridge 240. The valve block 242 canselect or permit one or more liquids within the reagent cartridge 240 toflow through the fluid network 238. For example, the valve block 242 caninclude 16 solenoid valves that have a compact arrangement. Eachsolenoid valve can control the flow of a fluid from a single reservoirbag. In some embodiments, the valve block 242 can permit two or moredifferent liquids to flow into the fluid network 238 at the same timethereby mixing the two or more different liquids. After leaving thevalve block 242, the fluid may flow through the main pump 244 and to thedebubbler 246. The debubbler 246 is configured to remove unwanted gasesthat have entered or been generated within the fluid network 238.

From the debubbler 246, fluid may flow to the 3-way valve 248 where thefluid is either directed to the biosensor cartridge 235 or bypassed tothe waste removal system 252. A flow of the fluid within the biosensorcartridge 235 may be at least partially controlled by the flowrestrictor 250 located downstream from the biosensor cartridge 235.Furthermore, the flow restrictor 250 and the main pump 244 maycoordinate with each other to control the flow of fluid across reactionsites and/or control the pressure within fluid network 238. Fluid mayflow through the biosensor cartridge 235 and onto the waste removalsystem 252. Optionally, fluid may flow through the purge pump 254 andinto, for example, a waste reservoir bag within the reagent cartridge240.

Also shown in FIG. 3, the workstation 200 may include a temperaturecontrol system, such as the temperature control system 110, that isconfigured to regulate or control a thermal environment of the differentcomponents and sub-systems of the workstation 200. The temperaturecontrol system 110 can include a reagent cooler 264 that is configuredto control a temperature of various fluids used by the workstation 200,and a thermocycler 266 that is configured to control a temperature ofthe biosensor cartridge 235. The thermocycler 266 can include a thermalelement (not shown) that interfaces with the biosensor cartridge.

Furthermore, the workstation 200 may include a system controller or SBSboard 260 that may have similar features as the system controller 104described above. The SBS board 260 may communicate with the variouscomponents and sub-systems of the workstation 200 as well as thebiosensor cartridge 235. Furthermore, the SBS board 260 may communicatewith remote systems to, for example, store data or receive commands fromthe remote systems. The workstation 200 may also include a touch screenuser interface 262 that is operatively coupled to the SBS board 260through a single-board computer (SBC) 272. The workstation 200 may alsoinclude a compact-flash (CF) drive and/or a hard drive 270 for storinguser data in addition to other software.

FIG. 4 provides various perspective views of the workstation 200. Inparticular embodiments, the workstation 200 is a stand-alone orbench-top unit such that all of the components described above withrespect to FIG. 3 may be held within the workstation housing 230.However, in other embodiments, the workstation housing 230 may containor partially contain only some of the components. The workstation 200permits a user to perform desired reactions within the biosensorcartridge 235 (FIG. 3) and, optionally, perform primary analysis ofobtained detection data of the desired reactions. The primary analysismay, for example, indicate to the user that the assay protocol wassuccessfully run and provide preliminary results of the assay protocol.The user interface 262 may be configured to receive user inputs andcommands as well as display information to the user. Also shown, theworkstation 200 may also include a system receptacle 212 that isconfigured to receive and engage the biosensor cartridge 235.

FIGS. 5 and 6 illustrate a biosensor cartridge 300 formed in accordancewith one embodiment that may be used with a bioassay system orworkstation, such as the bioassay system 100 (FIG. 1) and theworkstation 200 (FIG. 3). FIG. 5 is a partially exploded perspectiveview, and FIG. 6 provides plan views of opposite side surfaces 314 and315 of the biosensor cartridge 300. As shown, the biosensor cartridge300 is oriented with respect to a vertical or elevational axis 392 (FIG.5) and lateral axes 390 and 391. In the illustrated embodiment, thebiosensor cartridge 300 may include a microdevice 302. The biosensorcartridge 300 may also have a housing or casing 304 that encloses atleast a portion of the microdevice 302. In the illustrated embodiment,the casing 304 may include opposite shells 306 and 308 that couple toeach other along an interface. In some embodiments, the shells 306 and308 are readily separated thereby allowing a user or a machine toreplace components within the casing 304, such as the microdevice 302.For example, the shells 306 and 308 may form an interference fit (e.g.,snap-fit) or slidably engage each other in a locking arrangement. Theshells 306 and 308 may also use fasteners (e.g., screws or plugs) thatremovably couple the shells 306 and 308 together.

As shown, each of the shells 306 and 308 includes an opening or window310 and 312 (FIG. 6), respectively, that is sized and shaped to provideaccess to the microdevice 302 therein or permit the microdevice 302 toproject therethrough. As shown in FIG. 6, when the shells 306 and 308are coupled together, the biosensor cartridge 300 may have exterior sidesurfaces 314 and 315. In the illustrated embodiment, the side surfaces314 and 315 face in substantially opposite directions. For example, theside surfaces 314 and 315 may both face a direction along the verticalaxis 392.

The biosensor cartridge 300 may be sized and shaped to facilitatehandling by a user or machine and for being inserted into the systemreceptacle 212 (FIG. 4). For example, the biosensor cartridge may besubstantially rectangular or card-shaped. The biosensor cartridge 300may have a width W₁, a length L₁, and a thickness T₁ (as indicated bythe dashed lines in FIG. 5). The width W₁, the length L₁, and thethickness T₁ along with other features of the casing 304 and themicrodevice 302 may be configured to facilitate orienting the biosensorcartridge 300 when inserted into the system receptacle 212. Thedimensions can be, for example, in a range of 1 cm to 50 cm, 1 cm to 25cm, 1 cm to 10 cm, 5 cm to 50 cm, 5 cm to 25 cm, 5 cm to 10 cm, 10 cm to50 cm or 10 cm to 25 cm. For example, the biosensor cartridge 300 or thecasing 304 may have a tail end 348 (FIG. 6) that projects a substantialdistance away from the microdevice 302 to allow a user or machine togrip the biosensor cartridge 300.

FIG. 31 is a cross-section of the biosensor cartridge 300. As shown, themicrodevice 302 includes a device body 316 having opposite device sidesurfaces 330 and 332. The side surface 330 may be a portion of the sidesurface 314, and the side surface 332 may be a portion of the sidesurface 315. The device body 316 may include inlet and outlet ports 320and 322 along the same side surface 330 of the device body 316. Inalternative embodiments, the inlet and outlet ports 320 and 322 may beon opposite side surfaces. In other embodiments, at least one of theinlet and outlet ports 320 and 322 is located on an edge facing in adirection along the lateral axis 390 or the lateral axis 391 (FIG. 5).Also shown, the inlet and outlet ports 320 and 322 may have respectiveopenings 321 and 323.

The microdevice 302 can include a flow cell 334 that is mounted to abase substrate 335. The base substrate 335 may be a printed circuit,such as a PCB, that includes conductive pathways therethrough. Inalternative embodiments, the base substrate 335 is only configured toprovide structural support to the flow cell 334. The flow cell 334 andthe base substrate 335 may comprise the device body 316 and form asubstantially unitary structure. As shown, the base substrate 335comprises a planar body that may have lateral dimensions that are largerthan the lateral dimensions of the flow cell 334. For example, the basesubstrate 335 may have a length L₃, and the flow cell 334 may have alength L₄. The length L₃ may be greater than the length L₄. When theflow cell 334 is mounted onto the base substrate 335, the flow cell 334may be positioned such that the base substrate 335 extends beyond edgesof the flow cell 334. Although not shown, the widths of the basesubstrate 335 and the flow cell 334 may be similarly sized and shapedwith respect to each other.

Also shown, the device body 316 can be held within the casing 304 by aframe 317. The frame 317 may be attached to the casing 304 at the shell308 or the shell 306. The frame 317 extends around at least a portion ofa perimeter of the device body 316. In particular embodiments, the frame317 completely surrounds the perimeter. The frame 317 may also define awindow or opening 350 that is sized and shaped to permit the microdevice302 (or the flow cell 334) to extend therethrough. The opening 350 mayalso block or prevent the base substrate 335 from moving therethrough.More specifically, the opening 350 may be defined by an interior edge352 of the frame 317 and have a length L₆. The length L₆ may be lessthan the length L₃ of the base substrate 335.

In some embodiments the frame 317 holds the microdevice 302 in asubstantially stationary position with respect to the case 304. However,in other embodiments, the microdevice 302 may be moveable or floatablewithin a restricted space defined by the biosensor cartridge 300. Insuch embodiments, the moveable or floatable quality of the microdevice302 may permit the microdevice 302 to align with other components of theworkstation 200 to facilitate fluidicly, thermally, and/or electricallyengaging the workstation 200. For example, as shown in FIG. 31, interiorsurfaces of the frame 317 and the shell 308 may define a restrictedspace that has greater dimensions (e.g., length, height, and width) thanthe dimensions of the base substrate 335. In other words, the restrictedspace may provide additional spacing between the interior surfaces ofthe frame 317 and the shell 308. As such, the restricted space permitsthe microdevice 302 to shift and/or slightly rotate or pivot therein.For example, the microdevice 302 may be moveable in a lateral manneralong a plane formed by the lateral axes 390, 391 (i.e., the microdevicemay shift side-to-side). The microdevice also be moveable in a verticalmanner along the vertical axis 392 (i.e., the microdevice may shiftup-and-down). Furthermore, the microdevice 302 may also rotate or pivotabout a vertical axis that extends through the microdevice 302 and/orrotate or pivot about a lateral axis that extends through themicrodevice 302. Accordingly, the microdevice 302 may float with respectto the frame 317 or the casing 304.

However, the above description of the floatability of the microdevice302 is exemplary only. The microdevice 302 and, more specifically, thedevice body 316 may have various structural features or otherconfigurations that permit the microdevice 302 to float or move within arestricted space. Furthermore, in other embodiments, the microdevice 302is held in a stationary or fixed position with respect to the casing304.

Also shown in FIG. 31, the inlet and outlet ports 320 and 322 may beconfigured to removably engage nozzles of the workstation 200 tofluidicly couple a flow channel 327 of the biosensor cartridge 300 tothe workstation 200. When in operation, fluid may flow through themicrodevice 302 between the inlet and outlet ports 320 and 322 andrespective openings 321 and 323. More specifically, the fluid may flowalong the flow channel 327 within the biosensor cartridge 300 betweenthe inlet and outlet portions 320 and 322. As shown, the inlet andoutlet ports 320 and 322 may be separated from each other by a spacing325. The spacing 325 may extend along and provide access to anengagement area 328 of the common side surface 330. The engagement area328 may extend along and proximate to the flow channel within thebiosensor cartridge 300.

As will be described in greater detail below, the engagement area 328may be sized and shaped to interface with a thermal element of athermocycler to facilitate controlling a temperature of the fluid withinthe microdevice 302. At least a portion of the engagement area 328 thatextends along the flow channel may be a substantially flat surface. Theengagement area 328 may extend along a lateral plane that is parallel toa plane formed by lateral axes 390 and 391. The side surface 332 mayextend parallel to the engagement area 328.

As shown in FIG. 31, the device body 316 includes port projections 324and 326 having the inlet and outlet ports 320 and 322. The portprojections 324 and 326 may be separated from each other by the spacing325 and the engagement area 328. The port projections 324 and 326 mayproject away from the casing 304 or the engagement area 328 in asubstantially common direction (e.g., in a direction along the verticalaxis 392). When oriented in the system receptacle 212 (FIG. 4), the portprojections 324 and 326 may extend substantially parallel to agravitational force direction G. The port projections 324 and 326 maypermit the flow channel within the biosensor cartridge 300 to be shapedin a predetermined configuration to facilitate controlling a flow thefluid therein.

Also shown, the microdevice 302 may also include an array 336 ofelectrical mating contacts 338, which may also be referred to as devicecontacts or cartridge contacts. The mating contacts 338 may be locatedon the side surface 332 such that the fluidic access and electricalaccess to the microdevice 302 are provided on opposite sides of thedevice body 316 in the illustrated embodiment. The array 336 may beconfigured to engage an array of electrical contacts of the workstation200 to communicate with the workstation 200. In the illustratedembodiment, the cartridge contacts 338 are contact pads that interfacewith the electrical contacts of the workstation 200. The contact padsmay be substantially flush with a surface of the device side surface 332to allow the microdevice 302 to slidably engage the workstation 200.However, in alternative embodiments, the cartridge contacts 338 may belocated within sockets or may have beams or tails that project away fromthe device side surface 332. Furthermore, the cartridge contacts 338 maybe pogo pins.

To assemble the biosensor cartridge 300, the microdevice 302 may firstbe constructed by mounting the flow cell 334 to the base substrate 335.In the illustrated embodiment, the flow cell 334 includes an activitydetector that is communicatively coupled to electrical circuits withinthe base substrate 335. The flow cell 334 may be mounted using anadhesive that is sufficient to withstand the environment in which themicrodevice 302 operates. The microdevice 302 may then be positioned onan interior surface of the shell 306 such that the array 336 ofcartridge contacts 338 is accessible through the window 312. The frame317 may be mounted to the shell 308 so that the microdevice 302 isdisposed within the restricted space. Alternatively, the frame 317 maybe mounted to the shell 306 or integrally formed with the shell 306.

As shown, when the shells 306 and 308 are coupled together, the inletand outlet ports 320 and 322 and the engagement area 328 are on a commonside surface 314 of the biosensor cartridge 300. The port projections324 and 326 may extend through the window 310, and the array 336 ofcartridge contacts 338 may be accessible through the window 312.Furthermore, the microdevice 302 may be moveable or floatable withrespect to the casing 304.

Although the casing 304 is shown as being constructed from separateshells 306 and 308, in alternative embodiments, the housing or casing304 may be integrally formed with the microdevice 302. For example, thecomponents that comprise the microdevice 302 may also form the housingor casing of the biosensor cartridge. Such an alternative housing orcasing may have similar dimensions as the casing 304 described above.Thus, in some embodiments, the terms “biosensor cartridge” and“microdevice” may be used interchangeably.

Returning to FIGS. 5 and 6, the biosensor cartridge 300 may include anidentification component 340 to provide identification information ofthe biosensor cartridge 300. The identification component 340 mayfacilitate identification, tracking, and sorting of the biosensorcartridge 300. For example, the identification information provided bythe identification component 340 may be at least one of anidentification number, a date of manufacture, a lot number, and a typeof biosensor cartridge. The identification information may also relateto the biological or chemical substances inside the microdevice 302 andidentify, for example, a genome of interest of DNA fragments therein.The identification information may also provide one or more protocolsthat may be executed with the biosensor cartridge 300.

As shown, the identification component 340 may include a label 342 thatis affixed to the casing 304. The label 342 may include a visualindicator 344, such as a bar code. A user or system may scan theidentification component 340 to determine an alpha-numeric code or someother indicator. The user or system may have access to a table thatincludes a listing of codes or other indicators. The listing may thenassociate the scanned code or other indicator with the identificationinformation.

Alternatively or additionally, the identification component 340 mayinclude a transmitting device 346, such as an RFID tag physicallyassociated with the biosensor cartridge 300. The transmitting device 346may include an integrated circuit for storing and processing informationand/or modulating and demodulating a radio-frequency (RF) signal. Thetransmitting device 346 may also include an antenna for receiving andtransmitting the signal. In such embodiments where the transmittingdevice is an RFID tag, the RFID tag may be one of an active RFID tagthat has a battery for transmitting signals autonomously, a passive RFIDtags that requires an external source to provoke signal transmission,and a battery assisted passive (BAP) RFID tag that requires an externalsource to activate the RFID tag.

In some embodiments, the system receptacle 212 and the identificationcomponent 340 may automatically establish a communication link betweeneach other. For example, the system receptacle 212 may automaticallyscan the identification component 340 when the biosensor cartridge 300is inserted into the system receptacle 212. The system receptacle 212may also automatically receive the identification information from, forexample, the transmitting device 346 when the biosensor cartridge 300 iswithin a predetermined distance from the workstation 200. Theworkstation 200 may then communicate information to the user thatrelates to the biosensor cartridge 300. For example, the workstation 200may automatically notify the user that the biosensor cartridge 300 hasbeen inserted into the system receptacle 212. The workstation 200 maythen display information on the user interface 214 and/or automaticallyprompt the user to select certain options or features.

FIG. 7 shows a side view of an exemplary microdevice 400 formed inaccordance with one embodiment. The microdevice 400 may be used in ormay form a biosensor cartridge, such as the biosensor cartridge 300. Asshown, the microdevice 400 may include a flow cell 402 that includes aflow cover 404 mounted to sidewalls 406 (only one sidewall 406 is shownin FIG. 7). The flow cell 402 may also include a reaction substrate orsubstrate layer 408. The flow cell 402 may define a flow channel 410between the substrate layer 408 and the flow cover 404. As shown, theflow cover 404 includes two inlet channels 411 that are fluidiclycoupled to an inlet port (not shown). Fluid in the flow channel 410 mayflow out of the page to one or more outlet channels that are fluidiclycoupled to an outlet port (not shown).

In some embodiments, the flow cover 404 has an exterior surface 405 thatforms an engagement area that is sized and shaped to interface with athermal element (not shown) of a thermocycler. The flow cover 404 maycomprise a thermally conductive material that extends along the flowchannel 410. The flow cover 404 may form a cover wall 413 having auniform thickness T₂ in portion(s) that extend along the flow channel410. As such, thermal energy may more evenly transfer between a thermalelement and the fluid within the flow channel 410. In some embodiments,the flow cover 404 comprises a non-transparent material. Optionally, thematerial may be transparent in alternative embodiments. The flow cover404 may be attached to the sidewalls 406 using one or more attachmentmechanisms. For example, the flow cover 404 may be attached through aninterference fit or by using an adhesive or fastener.

The substrate layer 408 comprises a substrate material that facilitatesconducting desired reactions. As shown, the substrate layer 408 includesa substrate field 418 that includes a plurality of reaction sites 412where desired reactions may occur. In the illustrated embodiment, thereaction sites 412 are reaction chambers 414 that each defines aseparate spatial region or volume. The reaction chambers 414 may includeapertures 415 that open to the flow channel 410 so that thecorresponding reaction chambers 414 are in fluid communication with theflow channel 410. The reaction chambers 414 may be sized and shaped fora desired purpose. For example, the reaction chambers 414 may be sizedand shaped to accommodate a single DNA capture bead, such as those usedin known pyrosequencing protocols. In addition to the DNA bead, thereaction chambers 414 may hold smaller packing beads and/or beads havingreagents and enzymes immobilized thereon.

However, in alternative embodiments, the reaction sites are not requiredto be spatially or physically separated from each other. For example,reaction sites may be located on a planar surface in a predeterminedmanner (e.g., rows and columns of reactions sites) where each reactionsite comprises a portion of the planar surface. Examples of sucharrangements may be found on a microarray. In other embodiments,reaction sites may be located on a surface of an elongated channel. Thereaction sites may include randomly located clusters or colonies ofbiomolecules that are immobilized on the surface. As such, the reactionsites may be areas along a surface in addition to spatial regionsdefined by reaction chambers.

The microdevice 400 may also include an activity detector 420 that iscoupled to the flow cell 402. The activity detector 420 is configured todetect activity that is indicative of one or more desired reactionsoccurring within the microdevice 400. The activity detector 420 includesan array 425 of pixels 424 that are configured to detect activityindicative of a desired reaction from within or along the substratelayer 408. In some embodiments, a pixel area of each pixel 424 is lessthan about 50 microns. In more particular embodiments, the pixel area isless than about 10 microns. An average read noise of each pixel 424 maybe, for example, less than about 150 electrons. In more particularembodiments, the read noise may be less than about 5 electrons. Theresolution of the array 425 may be greater than about 0.5 Mpixels. Inmore specific embodiments, the resolution of the array 425 may begreater than about 5 Mpixels and, more particularly, greater than about10 Mpixels.

The array 425 of pixels 424 may have a fixed position relative to thesubstrate field 418. As shown in FIG. 7, the array 425 comprisessub-arrays 426 of pixels 424 in which the sub-arrays 426 are configuredto detect activity from a corresponding one reaction chamber 414. In theillustrated embodiment, the activity detector 420 is affixed to thesubstrate layer 408. Optionally, the activity detector 420 and thesubstrate layer 408 may be attached to each other through anintermediate layer 422. The intermediate layer 422 may comprise amaterial or have features that permit the pixels 424 to detect theactivity indicative of the desired reaction.

In the illustrated embodiment, the activity detector 420 includes amicrocircuit arrangement, such as the microcircuit arrangement describedin U.S. Pat. No. 7,595,883, which is incorporated herein by reference inthe entirety. More specifically, the activity detector 420 may comprisean integrated circuit having a planar array of photodetectors (i.e., thepixels 424) arranged on a side 428 of a detector substrate 430. Thephotodetectors may be configured to detect light signals that areemitted from within the reaction chambers 414. The side 428 mayinterface with the substrate layer 408. Circuitry formed within thedetector substrate 430 may be configured for at least one of signalamplification, digitization, storage, and processing. The circuitry maycollect and analyze the detected activity and generate signals forcommunicating detection data to a bioassay system. The signals may betransmitted through electrical contacts of the microdevice 400 or abiosensor cartridge, such as the cartridge contacts 338 (FIG. 6). Thecircuitry may also perform additional analog and/or digital signalprocessing. As such, the array 425 of pixels 424 may be communicativelycoupled to the electrical contacts that interface with a bioassaysystem. Furthermore, the circuitry may also include an identificationcomponent or module that is configured to provide identificationinformation to the bioassay system.

FIGS. 8-10 illustrate exemplary activity detectors in greater detail.FIG. 8 is a perspective view of a portion of the substrate field 418. Atleast a portion of the intermediate layer 422 (FIG. 7) may includewire-bonding for attaching the substrate layer 408 (FIG. 7) to the side428 of the activity detector 420. The substrate layer 408 may bedeposited onto the wire-bonding of the intermediate layer 422. Thesubstrate layer 408 may comprise a polymer material, such as SUB. In theillustrated embodiment, the reaction chambers 414 have a predeterminedpattern along the substrate layer 408 (i.e., the reaction chambers 414form an array). For example, as shown in FIG. 8, the reaction chambers414 may have a regular hexagonal-shape cross-section and form ahoneycomb-like lattice along the substrate layer 408. Each reactionchamber 414 may be separated from adjacent reaction chambers 414 bychamber walls 438. In the illustrated embodiment, the chamber walls 438have a common thickness. Optionally, interior surfaces of the chamberwalls 438 may be hydrophilic or hydrophobic. Furthermore, an exteriorsurface of the chamber walls 438 that faces away from the activitydetector 420 may partially define the flow channel 410. The exteriorsurface may extend along a plane to facilitate providing a desired flowof fluid through the flow channel 410 (FIG. 7). The exterior surface mayalso be hydrophilic or hydrophobic.

FIG. 9 is a plan view of a single reaction chamber 414 and the pixels424 within the reaction chamber 414. In some embodiments, the substratelayer 408 (FIG. 7) has a fixed position relative to the activitydetector 420 so that the reaction chambers 414 have known spatiallocations relative to at least one predetermined pixel 424. The at leastone predetermined pixel 424 detects activity of the desired reactionsfrom the reaction chamber 414. As such, the reaction chambers 414 may beassigned to at least one pixel 424. To this end, the circuitry of theactivity detector 420 may include kernels that automatically associatedetection signals provided by predetermined pixels 424 with the assignedreaction chambers 414. By way of example, when detection signals aregenerated by pixels 424 shown in FIG. 9, the detection signals willautomatically be associated with the reaction chamber 414 shown in FIG.9. Such a configuration may facilitate processing and analyzing thedetection data. For instance, the detection signals from one reactionchamber may automatically be located at a certain position on an image.

Also shown in FIG. 9, in some embodiments, a detection surface of thepixels 424 is at least partially covered or obstructed such that thecovered detection surface is unable to detect activity. Morespecifically, the reaction chamber 414 has a plurality of pixels 424,including partially covered pixels 424A and 424B and an entirely exposedpixel 424C. The pixels 424A and 424B are partially covered by thechamber walls 438 of the reaction chamber 414. In some embodiments,kernels of the circuitry of the activity detector 420 may modify valuesof the detected activity to provide a better representation of thedetected activity within the reaction chamber 414. For example, thecircuitry may include a kernel for weighting the values of the activitydetected by the pixels 424A and 424B.

FIG. 10 provides a schematic illustration of an exemplary activitydetector 432 that may be used in various embodiments described herein.For example, the activity detector 432 may be used as the activitydetector 420 shown in FIG. 7. The activity detector 432 may bemanufactured as a single chip through a CMOS-based fabricationprocesses. As shown, the activity detector 432 includes atwo-dimensional array 440 of photodiodes or pixels 436 that arecommunicatively coupled to circuitry 434. The array 440 iscommunicatively coupled to a row decoder 442 and a column amplifier ordecoder 444. The column amplifier 444 is also communicatively coupled toa column analog-to-digital converter (Column ADC/Mux) 446. Othercircuitry may be coupled to the above components, including a digitalsignal processor and memory.

FIG. 10 also includes a schematic illustration of a photodiode 436. Insome embodiments, the photodiode 436 may be configured to detect apredetermined wavelength of light that is indicative of the desiredreactions. As shown, the photodiode 436 may include a P-type substratehaving an N-type doping region.

FIGS. 11 and 12 illustrate a fiber-optic faceplate 450 that may be usedas the substrate layer 408 (FIG. 7) in alternative embodiments. FIG. 11is an image showing a plan view of the faceplate 450, and FIG. 12 is across-section of the faceplate 450 that is interfacing with an activitydetector 452. As shown in FIG. 12, the activity detector 452 may besimilar to the activity detector 420 (FIG. 7) or, in a more particularembodiment, the activity detector 436 (FIG. 10). The faceplate 450 maybe manufactured from a fiber-optic bundle comprising a plurality ofoptical fibers of a polymer material (e.g., SU8) that are fused togetherand cut to form a substrate layer or plate having a thickness T₃. Thefaceplate 450 may be subsequently etched or machined to form a pluralityof reaction chambers 454. The reaction chamber 454 may have similardimensions and functions as the reaction chamber 414 (FIG. 7) describedabove. As shown, optical fibers 458 below the reaction chamber 454 maytransmit light signals that are emitted from within the reaction chamber454 to a pixel 456 of the activity detector 452. In some embodiments,circuitry of the activity detector 452 may assign at least one pixel 456to the reaction chamber 454 to facilitate subsequent processing oranalysis.

However, the activity detector 420 is not limited to the aboveconstructions or uses as described above. In alternative embodiments,the activity detector may take other forms. For example, the activitydetector may comprise a CCD device, such as a CCD camera, that iscoupled to a flow cell or is moved to interface with a flow cell havingreaction sites therein. In other embodiments, the activity detector maybe a CMOS-fabricated sensor, including chemically sensitive field effecttransistors (chemFET), ion-sensitive field effect transistors (ISFET),and/or metal oxide semiconductor field effect transistors (MOSFET). Suchembodiments may include an array of field effect transistors (FET's)that may be configured to detect a change in electrical propertieswithin the reaction chambers. For example, the FET's may detect at leastone of a presence and concentration change of various analytes. By wayof example, the array of FET's may monitor changes in hydrogen ionconcentration. Such activity detectors are described in greater detailis U.S. Patent Application Publication No. 2009/0127589, which isincorporated by reference in the entirety for the use of understandingsuch FET arrays.

FIGS. 13-22 illustrate different flow covers that may be used in variousembodiments, such as in the biosensor cartridge 300 (FIG. 5) ormicrodevice 400 (FIG. 7). Each of the flow covers in FIGS. 13-22 includeinlet and outlet ports configured to fluidicly couple the correspondingflow cover (or flow cell) to a fluid network. Embodiments describedherein may facilitate providing a desired flow of fluid across one ormore reaction sites. For example, embodiments described herein mayfacilitate providing a uniform flow of fluid across the reaction sites.In some embodiments, flow cells may include a flow cover that isintegrally formed with a substrate layer. In other embodiments, the flowcover may be coupled or mounted to the substrate layer. FIGS. 13-22illustrate such flow covers. Furthermore, it is understood that thevarious features described below with respect to the flow covers mayalso be incorporated into flow cells.

FIG. 13 is a top perspective view of a flow cover 500 illustrating aflow channel 502 in phantom, and FIG. 14 is a bottom perspective view ofthe flow cover 500. The flow cover 500 may have a mounting surface 501(FIG. 14) that is configured to be mounted to another element orcomponent to form a biosensor cartridge or microdevice. For example, theflow cover 500 may be mounted to a substrate layer or some other base.

As shown in FIG. 13, the flow channel 502 extends between inlet andoutlet ports 504 and 506 and defines a volume in which fluid may flowtherebetween. As shown, the flow channel 502 includes an input region510 that receives fluid through the inlet port 504, a diffuser region511 that includes one or more inlet channels 516, a field region 512that is configured to direct the fluid across a substrate field (notshown) that includes one or more reaction sites, a collector region 513that receives the fluid from the field region 512, and an output region514 that delivers the fluid to the outlet port 506. Each of the channelregions 510-514 of the flow channel 502 may be sized and shaped withrespect to each other to provide a desired flow of fluid across thesubstrate field.

As shown, the field region 512 of the flow channel 502 may have a lengthL₂ that extends along a direction of the flow of the fluid (indicated bythe arrows F), a width W₂ that extends perpendicular to the length L₂,and a height H₂. The mounting surface 501 (FIG. 14) may form a perimeterof the field region 512. In the flow cover 500, the field region 512 maybe substantially rectangular. For example, each dimension (i.e., thelength L₂, width W₂, and height H₂) may be substantially uniformthroughout the field region 512. However, in alternative embodiments,the field region 512 may have different shapes and dimensions.Furthermore, each dimension may change as said dimension extendslengthwise or widthwise.

Fluid may enter through the inlet port 504 and into the input region510. The diffuser region 511 receives the fluid and separates the volumeto a plurality of inlet channels 516. The inlet channels 516 deliver thefluid to the field region 512. As shown, the inlet channels 516 may bedistributed across the width W₂ of the field region 512. The fluid flowsacross the substrate field (not shown) and is removed by outlet channels518 of the collector region 513. The fluid is then removed from the flowcover 500 through the output region 514.

In some embodiments, the input and output regions 510 and 514 extend ina direction that is perpendicular to the field region 512. Morespecifically, in operation the fluid may flow through the input andoutput regions 510 and 514 in a direction that is parallel to agravitational force direction G and perpendicular to a flow direction ofthe field region 512 (i.e., a general direction in which the fluid flowsthrough the field region 512). Moreover, the fluid may flow through theinput and output regions 510 and 514 in a direction that isperpendicular to a flow direction through the diffuser and collectorregions 511 and 513.

The flow cover 500 may be integrally formed, for example, by aninjection molding process. More specifically, rods or columns may extendthrough a void of a molding apparatus where the regions 510, 511, 513,and 514 are to be located. A block may extend into the void as well toform the field region 512. After a resin is injected into the void ofthe molding apparatus, the rods and block may be removed thereby leavingcavities that are used to form the channel regions 510-514. Pluggingelements 520 may then be formed or inserted into the various cavities todefine the various channel regions 510-514.

FIG. 15 is a top perspective view of a flow cover 522 illustrating aflow channel 524 in phantom. As shown, the flow channel 524 extendsbetween inlet and outlet ports 526 and 528 and includes a plurality ofchannel regions, including a diffuser region 530, a field region 532,and a collector region 534. The diffuser region 530 is shaped todistribute the fluid to the field region 532 and may be oriented suchthat the flow direction is parallel to a vertical axis 590. The diffuserregion 530 has first and second flow cross-sections C₁ and C₂ that aretaken perpendicular to the vertical axis 590. The term “flowcross-section,” as used herein, is a cross-section of a fluidic channelthat is taken substantially transverse to a direction of the flow offluid. For example, the flow of fluid through flow cross-sections C₁ andC₂ in FIG. 15 is generally out of (or into) the page.

As shown, the flow cross-section C₁ is located closer to the inlet port526, and the flow cross-section C₂ is located closer to the field region532. In the illustrated embodiment, at least one cross-sectionaldimension increases as the diffuser region 530 extends toward the fieldregion 532. More specifically, a width W_(D) of the diffuser region 530increases as the diffuser region 530 extends toward the field region532. When the diffuser region 530 reaches the field region 532, thediffuser and field regions 530 and 532 may have substantially the samewidth W_(D3). Also shown, the collector region 534 may be similarlyshape as the diffuser region 530.

FIGS. 16 and 17 provide a bottom view and a perspective view,respectively, of a flow cover 540. The flow cover 540 may have similarfeatures as the flow cover 522. However, as shown in FIG. 16, a diffuserregion 542 and a collector region 544 may have different dimensions atrespective openings 543 and 545. More specifically, the opening 545 ofthe collector region 544 may have a greater width W_(D2) than a widthW_(D1) of the opening 543 of the diffuser region 542.

FIG. 18 is a top perspective view of a flow cover 550. In someembodiments, field regions of the flow channel may be shaped to diffuse(or expand) the flow of fluid or to compress (or contract) the flow offluid. For example, the flow cover 550 includes an inlet channel 552 ofan input region 554 that provides fluid to a field region 556. Fluid maybe removed from the field region 556 through an outlet channel 558 of anoutput region 560. As shown, the field region 556 is oriented in asubstantially horizontal manner relative to a gravitational forcedirection G. The field region 556 may be diamond-shaped such that theflow channel has an increasing cross-section as the fluid initiallyflows away from the inlet channel 552. The field region 556 may have auniform cross-section for a middle portion of the field region 556 asthe fluid flows therethrough, and then begin to decrease when the fluidis proximate to the outlet channel 558. As such, the flow coversdescribed herein may have horizontal diffuser regions and verticaldiffuser regions as well as horizontal collector regions and verticalcollector regions.

FIG. 19 is a top perspective view of a flow cover 562. In previouslydescribed embodiments, a flow cross-section taken perpendicular to theflow of the fluid may have a height that remained substantially equal toother cross-sections. However, the flow cover 562 includes a flowchannel 564 where a height in cross-sections taken perpendicular to theflow of fluid changes. As shown in flow cross-section C₃, a height H₃ ofthe cross-section varies therealong. Furthermore, dimensions of the flowcross-section C₄ may also be different from the dimensions of the flowcross-section C₃. For example, the height H₄ may be greater than theheight H₃. Accordingly, embodiments of flow covers and flow cellsdescribed herein may have flow channels and, more specifically, fieldregions of the flow channels with varying three-dimensional shapes tocontrol a flow of fluid as desired.

FIG. 20 illustrates an exemplary embodiment of a planar flow cover 570.The flow cover 570 may have a substantially rectangular or block shapeand include a height H₅, a width W₅, and a length L₅ that aresubstantially uniform. As shown, the flow cover 570 may have inlet andoutlet ports 572 and 574 that are directly adjacent to a field region576. As such, fluid entering through the inlet port 572 may immediatelyenter the field region 576, and fluid exiting the field region 576 mayimmediately exit the flow cover 570 through the outlet port 574. In theillustrated embodiment, the field region 576 may have similar dimensionsas the field region 564. However, in alternative embodiments, the fieldregion 576 may have other dimensions.

FIGS. 21 and 22 are top and bottom views of a biosensor cartridge 580having a microdevice 582 that comprises the flow cover 570 (FIG. 21)mounted to a base substrate 584 (FIG. 22). As shown, the base substrate584 includes an exterior side surface 586 having an array of electricalcontacts 588 thereon. The microdevice 582 may be held by a housing 585.More specifically, the microdevice 582 may be confined within arestricted space defined by the housing 585. A cavity 589 of the housing585 may hold the microdevice 582 such that the side surface 586 and anopposite side surface 587 do not clear a surface of the housing 585. Insuch embodiments, the biosensor cartridge 580 may be inserted into asystem receptacle (not shown) without the microdevice 582 snagging orcatching a portion of the system receptacle.

FIGS. 23-27 illustrate the system receptacle 212 in greater detail. FIG.23 is a perspective view of the system receptacle 212 before a biosensorcartridge 600 is inserted into the system receptacle 212. The biosensorcartridge 600 may have similar features as described elsewhere, such aswith respect to the biosensor cartridges 300 and 580; with respect tothe microdevices 102, 235, 302, 400, and 582; with respect to the flowcell 334; and with respect to the flow covers 404, 500, 522, 540, 550,562, and 570. As shown, the system receptacle 212 is oriented withrespect to a longitudinal axis 690, a lateral axis 692, and a verticalaxis 694.

As shown in FIG. 23, the system receptacle 212 includes a firstreceptacle sub-assembly 602, a second receptacle sub-assembly 604, andan actuation device 606 that is operatively coupled to the secondreceptacle sub-assembly 604. The first and second receptaclesub-assemblies 602 and 604 are vertically stacked with respect to eachother and spaced apart in an unengaged position. The system receptacle212 includes a cartridge slot 608 that may receive the biosensorcartridge 600. The first and second receptacle sub-assemblies 602 and604 are configured to be moved toward each other into an engagedposition. In the engaged position, the biosensor cartridge 600 may bemechanically, electrically, and fluidicly coupled to the workstation 200(FIG. 3). For example, in the illustrated embodiment, the firstreceptacle sub-assembly 602 holds the biosensor cartridge 600 in apredetermined position. The actuation device 606 is configured to movethe second receptacle sub-assembly 604 in a linear manner along thevertical axis into the engaged position with the first receptaclesub-assembly 602 where the biosensor cartridge 600 may be mechanically,electrically, and fluidicly coupled to the workstation 200.

In the illustrated embodiment, the first receptacle sub-assembly 602holds the biosensor cartridge 600 in the predetermined position and, assuch, is hereinafter referred to as the alignment assembly 602. Thesecond receptacle sub-assembly 604 is moved to engage the alignmentassembly 602 and, as such, is hereinafter referred to as the mountingassembly 604. However, in alternative embodiments, the first receptaclesub-assembly 602 may be moved toward the second receptacle sub-assembly604 or both the first and second receptacle sub-assemblies 602 and 604may be moved toward each other. Also shown in FIG. 23, a pair ofconduits 632 and 634 may be affixed to the mounting assembly 604. Theconduits 632 and 634 may be fluidicly coupled to the fluid network ofthe workstation 200.

The actuation device 606 may be coupled to the mounting assembly 604through a joint assembly 610. The joint assembly 610 is configured topermit the mounting assembly 604 to pivot or shift when moved toward theengaged position so that the mounting assembly 604 may be aligned whenengaging the biosensor cartridge 600. In the illustrated embodiment, thejoint assembly 610 includes a rod 612 and a pair of rotatable links 614and 616 that are interconnected by the rod 612. The actuation device 606may be coupled to the rod 612, and the rotatable links 614 and 616 maybe coupled to the mounting assembly 604. The rotatable links 614 and 616may have inward projections 648 (FIG. 24) that engage the mountingassembly 604. In some embodiments, the inward projections 648 may permitthe mounting assembly 604 to shift along an axis that is parallel to thelateral axis 692 and the alignment axis 695. Furthermore, in someembodiments, the inward projections 648 may permit the mounting assembly604 to rotate along such an axis.

The mounting assembly 604 may also include a plurality of bores 622 thatextend through the mounting assembly 604 along the vertical axis 694.The system receptacle 212 may include a plurality of alignment pins 620that extend through corresponding bores 622. The alignment pins 620 areattached to the alignment assembly 602 at one end and have a stopper 624at an opposite end. The bores 622 may be shaped relative to thecorresponding alignment pins 620 to permit the mounting assembly 604 topivot or shift when moved toward the engaged position. For example, thebores 622 may have a cross-sectional diameter that is slightly greaterthan a cross-sectional diameter of the alignment pins 620.

To mount the mounting assembly 604 to the alignment assembly 602 (i.e.,move the mounting assembly 604 from the unengaged position to theengaged position), the actuation device 606 may move the mountingassembly 604 in a linear manner toward the alignment assembly 602. Asthe mounting assembly 604 approaches the alignment assembly 602, themounting assembly 604 may engage components or portions of the alignmentassembly 602 and/or the biosensor cartridge 600. If the mountingassembly 604 is misaligned with the biosensor cartridge 600 and/or thealignment assembly 602, the mounting assembly 604 may at least one of(a) shift along a plane formed by the longitudinal axis 690 and thelateral axis 692 and (b) pivot about the alignment axis 695 that extendsparallel to the lateral axis 692.

FIG. 24 is a bottom perspective view of the mounting assembly 604. Themounting assembly 604 may include a mating face 640 that engages thebiosensor cartridge 600 (FIG. 23) and the alignment assembly 602 (FIG.23). As shown, the mating face 640 may include a thermal module orelement 641 and nozzles 642 and 644 of the conduits 632 and 634 (FIG.23). The thermal element 641 includes a surface 650 and is configured tointerface with an engagement area of the biosensor cartridge 600 totransfer or absorb heat from the biosensor cartridge. The nozzles 642and 644 are configured to be inserted into inlet and outlet ports 662and 664 of the biosensor cartridge 600 to fluidicly couple theworkstation 200 (FIG. 3) to the biosensor cartridge 600.

FIG. 25 is a perspective view of the alignment assembly 602. Thealignment assembly 602 may also include a mating face 652 that engagesthe mounting assembly 604. The alignment assembly 602 may include tracksor guiderails 654 and 655 that engage opposite edges 656 and 657 (FIG.24) of a housing or casing 658 of the biosensor cartridge 600. When thebiosensor cartridge 600 is inserted into the cartridge slot 608, theguiderails 654 and 655 may direct the biosensor cartridge 600 to adesired slot position as shown in FIG. 25. In the slot position, thebiosensor cartridge 600 may be oriented to engage the mating face 640(FIG. 24) of the mounting assembly 604. More specifically, an engagementarea 660 of the biosensor cartridge 600 may face and be positioned toreceive the thermal element 641, and inlet and outlet ports 662 and 664of the biosensor cartridge 600 may open to and be positioned to receivethe nozzles 642 and 644.

FIGS. 26 and 27 are cross-sections of the biosensor cartridge 600 andthe system receptacle 212 illustrating the mounting and alignmentassemblies 604 and 602 in unengaged and engaged positions, respectively.In both FIGS. 26 and 27, the biosensor cartridge 600 is in the desiredslot position. As shown, the system receptacle 212 may also include anelectrical connector 666 that electrically engages the biosensorcartridge 600 so that the workstation 200 (FIG. 3) may communicateand/or provide power to the biosensor cartridge 600. For example, thebiosensor cartridge 600 may be able to provide detection data regardingany detected activity of desired reactions that occurred in thebiosensor cartridge 600. In some embodiments, the electrical connector666 is located on a first side surface 668 of the biosensor cartridge600 and the nozzles 642 and 644 and/or the thermal element 641 arelocated on an opposite second side surface 669 (FIG. 26). The systemreceptacle 212 may be configured to electrically engage the biosensorcartridge 600 before fluidicly engaging the biosensor cartridge 600.Alternatively, the system receptacle 212 may be configured to fluidiclyengage the biosensor cartridge 600 before electrically engaging thebiosensor cartridge 600. Moreover, the system receptacle 212 may beconfigured to electrically and fluidicly engage the biosensor cartridge600 at substantially the same time.

The electrical connector 666 may include a mating side 670 that includesan array 672 of electrical contacts 674 (FIG. 26) (hereinafter referredto as system contacts) that electrically engage electrical contacts (notshown) (hereinafter referred to as cartridge contacts) of the biosensorcartridge 600. In particular embodiments, the system contacts 674 mayprovide a resilient spring force toward the first side surface 668. Forexample, the system contacts 674 may include pogo pin contacts orresilient beams that flex to and from the mating side 670 in a directionalong the vertical axis 694. Furthermore, the system contacts 674 mayinclude a wipe surface that is sized and shaped to permit somemisalignment between one system contact 674 and the correspondingcartridge contact.

In particular embodiments, the electrical connector 666 is moveable toand from the biosensor cartridge 600. For example, the electricalconnector 666 may be moved in an axial direction (i.e., along thevertical axis 694) to and from the biosensor cartridge 600. Morespecifically, the electrical connector 666 may be moveable from anunmated position as shown in FIG. 26, wherein the system contacts 674are spaced apart from cartridge contacts of the biosensor cartridge 600,to a mated position as shown in FIG. 27, wherein the system contacts 674and the cartridge contacts are electrically engaged. In someembodiments, the electrical connector 666 is moved through an opening orwindow 680 of the housing 658 to engage the cartridge contacts.

Also shown in FIGS. 26 and 27, the conduits 632 and 634 (along with thecorresponding nozzles 642 and 644) may be separately or independentlymoveable along the vertical axis 694 to facilitate fluidicly couplingthe biosensor cartridge 600 to the fluid network. The mounting assembly604 may include resilient springs 682 and 684 that reside withinrespective cavities 686 and 688. The resilient springs 682 and 684 areconfigured to engage ledges of the conduits 632 and 634 to resistmovement in a direction away from the biosensor cartridge 600. As shownin FIG. 26, in the relaxed (i.e., unengaged position), the nozzles 642and 644 extend a distance D₁ away from the mating face 640.

Likewise, the thermal element 641 may be separately or independentlymoveable along the vertical axis 694 to facilitate maintaining a thermalengagement with respect to the engagement area 660 (FIG. 26) of thebiosensor cartridge 600. The mounting assembly 604 may include resilientsprings 691 and 693 (FIG. 26) that surround mounting posts that supportthe thermal element 641. In the relaxed (i.e., unengaged position), thethermal element 641 extends a distance D₂ away from the mating face 640.The resilient springs 691 and 693 may resist movement of the thermalelement 641 and provide a reactive force that facilitates maintainingthe thermal interface between the engagement area 660 and the thermalelement 641.

In the illustrated embodiment, after the biosensor cartridge 600 isinserted into the cartridge slot 608 (FIG. 23) and moved to the slotposition, the electrical connector 666 may be moved to an engagedposition with respect to the first side surface 668 of the biosensorcartridge in which the system contacts 674 electrically engage thecartridge contacts. In such embodiments where the system contacts 674project from the mating side 670 and provide a resilient spring forcetoward the first side surface 668, the system contacts 674 may initiallyengage the cartridge contacts before the electrical connector 666 hasbeen fully moved into the engaged position. If the surfaces of thebiosensor cartridge 600 and the electrical connector 666 do not fullyengage each other along the interface, the system contacts 674 mayfacilitate electrically engaging and maintaining the electricalconnection throughout operation of the workstation 200. Before themating face 640 is mounted to the biosensor cartridge 600, in someembodiments, a system controller may notify a user that the electricalconnector 666 has properly engaged the biosensor cartridge 600. However,if the electrical connector 666 has improperly engaged the biosensorcartridge 600, the system controller may notify the user that theelectrical engagement between the electrical connector 666 and thebiosensor cartridge is improper.

As described above, the mating face 640 of the mounting assembly 604 maymount the biosensor cartridge 600 after, before, or at substantially thesame time as when the electrical connector 666 has engaged the cartridgecontacts. The mating face 640 may be moved toward the biosensorcartridge 600 by the actuation device 606 (FIG. 23). The nozzles 642 and644 may engage the inlet and outlet ports 662 and 664, respectively, ofthe biosensor cartridge 600 before the mounting assembly 604 has movedfully into the engaged position. At this time, the nozzles 642 and 644may be pushed away from the second side surface 669 of the biosensorcartridge 600 (i.e., in a direction opposite to the mounting direction).The resilient springs 682 and 684 may resist the movement. As shown inFIG. 27, stored (or potential) energy of the resilient springs 682 and684 may facilitate maintaining the fluidic connection between the inletand outlet ports 662 and 664 and the nozzles 642 and 644 when themounting assembly 604 is in the fully engaged position with respect tothe biosensor cartridge 600 and the alignment assembly 602. For example,the stored energy may maintain the fluidic connection during flowpressure changes of an assay protocol.

Furthermore, the thermal element 641 may press against the engagementarea 660 of the biosensor cartridge when the mounting assembly 604 ismoved into the engaged position. The resilient springs 691 and 693 mayresist movement of the thermal element 641 in a direction opposite tothe mounting direction (or away from the biosensor cartridge 600). Inthe engaged position, stored (or potential) energy of the resilientsprings 691 and 693 may facilitate maintaining the thermal engagementbetween the thermal element and the engagement area 660 of the biosensorcartridge 600.

In some embodiments, the microdevice 628 of the biosensor cartridge 600may be floatable within the housing 658. Dimensions of the restrictedspace of the housing 658 that holds the microdevice 628 may be greaterthan the dimensions of the microdevice. In such embodiments, themicrodevice may slide within the housing 658 to facilitate properlyaligning the biosensor cartridge 600. For example, if the nozzles 642and 644 are misaligned with respect to openings of the inlet and outletports 662 and 664, the microdevice 628 may slide in a lateral mannerinto a properly aligned position.

Accordingly, embodiments described herein may comprise one or morefeatures that permit independent movement of components of the systemreceptacle to facilitate fluidicly, thermally, and/or electricallyengaging biosensor cartridges. Such independent movement may providetolerance for mating different elements. For example, embodimentsdescribed herein may include the joint assembly 610 to permit themounting assembly 604 to pivot or shift so that the nozzles 642 and 644and the thermal element 641 are properly aligned with the biosensorcartridge 600. Furthermore, embodiments described herein may includeresilient springs 682 and 684 that permit the nozzles 642 and 644,respectively, to separately move along the vertical axis 694. Similarly,embodiments may also include resilient springs 691 and 693 that permitthe thermal element 641 to separately move along the vertical axis 694.In addition, the electrical connector 666 may be moveable along thevertical axis 694 and may also include resilient system contacts 674 theproject a distance away from the electrical connector 666. The systemcontacts 674 and/or the cartridge contacts of the biosensor cartridge600 may have a sufficient wipe distance to tolerate some misalignmentbetween corresponding contacts. Furthermore, the microdevice 628 and/orthe biosensor cartridge 600 may also be independently moveable to permitthe system receptacle 212 to move the biosensor cartridge 600 when inthe desired slot position.

In alternative embodiments, other mounting mechanisms may be used. Forexample, the mounting assembly 604 is not required to move in a linearmanner to engage the alignment assembly 602. The mounting assembly 604may be rotated about an axis to engage the alignment assembly 602 in amanner similar to a door being moved from an open to a closed position.In addition, the mounting assembly 604 may be independently moveablesuch that a user may mount the mounting assembly 604 onto the alignmentassembly 602 after the biosensor cartridge 600 has been placed in thepredetermined orientation or position.

Furthermore, in alternative embodiments, the thermal element may beconfigured to approach and engage the biosensor cartridge 600 along thefirst side surface 668. More specifically, the thermal element and thesystem contacts may engage a common side of the biosensor cartridge 600.

In addition, the resilient force generated by the resilient springs 682,684, 691, and 693 may be generated by other mechanisms. For example, apneumatic system may be operatively coupled to the thermal element 641and nozzles 642 and 644 used to provide the resilient force.

Although the system receptacle 212 was described above with respect tobeing part of the workstation 200, the system receptacle 212 may also beconfigured to operate with other bioassay systems. Furthermore, thesystem receptacle 212 is not required to be located within a workstationhousing, but may be a separate apparatus that is remotely located fromthe workstation.

FIGS. 28, 29, and 30 illustrate a fluid storage unit 700 that may beused to store fluids for the workstation 200 (FIG. 3). FIGS. 28 and 29provide a partial perspective view and a top plan view of the storageunit 700 with a lid (not shown) of the storage unit 700 removed. Asshown, the storage unit 700 includes a bag container 702, a plurality offluid reservoir bags 704, and a waste reservoir bag 706 (FIG. 29). Inthe illustrated embodiment, a fluidic control system is configured toremove fluid (e.g., reagents, water, buffer solution, cleaning solution,and the like) from the corresponding reservoir bags 704 to a biosensorcartridge. After flowing through the biosensor cartridge, the fluid maybe removed and directed into the waste reservoir bag 706. Only one wastereservoir bag 706 is shown in FIG. 29, but additional waste reservoirbags may be used.

As shown in FIG. 28, the storage unit 700 may include a manifoldassembly 710 comprising a plurality of tubes 712 arranged along a side713 of the bag container 702. The tubes 712 are configured to beinserted into the reservoir bags 704 to fluidicly couple the fluids ofthe reservoir bags 704 to the fluid network. The tubes 712 may be heldby an interference fit formed by the tubes 712 and slots 714 of the bagcontainer 702 (e.g., the tubes 712 may be snap-fit into the slots 714).Adjacent slots 714 may extend from a top edge 716 of the bag container702 at different distances so that the tubes 712 may have a staggeredrelationship with respect to each other as shown in FIG. 28. Althoughnot shown, when the lid is positioned over a top of the bag container702, the lid may facilitate holding the tubes 712 in a desired position.The tubes 712 may project from the side 713 of the bag container 702.

FIG. 30 is a side view of the exemplary reservoir bag 704 that is formedin accordance with one embodiment. As shown, the reservoir bag 704 mayhave a top end 720, a bottom end 722, and a height 724 that extendstherebetween. The reservoir bag 704 may be defined by edges 741-644.When in operation, the height 724 may extend in a direction along thegravitational force G. In the illustrated embodiment, the reservoir bag704 includes a pair of opposite flexible walls 726 and 728 that bondedtogether. However, in alternative embodiments, the reservoir bag 704 mayinclude only one wall that includes the features described herein. Theflexible walls 726 and 728 may define a variable volume for holding afluid. For example, the flexible walls 726 and 728 may collapse towardeach other as fluid is removed from the volume. As shown, the volumeincludes a main storage portion 730, a flow path portion 732, and abridge portion 734. The main storage portion 730 and the flow pathportion 732 are in fluid communication with each other through thebridge portion 734. Furthermore, the reservoir bag 704 may include a bagopening 736 that is located proximate to the top end 720. The bagopening 736 is configured to fluidicly engage a corresponding one of thetubes 712.

As shown in FIG. 30, the reservoir bag 704 includes a partition 740where the flexible walls 726 and 728 are bonded together that extendsfrom the top end 720 (or top edge 741) and toward the bottom end 722 (orbottom edge 743). The partition 740 may extend to a distal tip 745 thatis proximate to the bottom end 722. As shown, the bridge portion 734 islocated between the distal tip 745 and the bottom end 722. In theillustrated embodiment, the main storage portion 730 of the volume isgreater than the flow path portion 732 of the volume. Furthermore, thebag opening 736 may be located at distance D₂ away from the top end 720or top edge 741. The distance D₂ may be configured to permit some air tocollect proximate to the top end 720 in the flow path portion 732without the air being removed through the bag opening 736.

Accordingly, when the fluid is removed from the reservoir bag 704, thefluid flowing from the main storage portion 730 flows to the flow pathportion 732 through the bridge portion 734. Fluid from the flow pathportion 732 flows through the bag opening 736 to the fluid network. Assuch, fluid is drawn from proximate to the bottom end 722 to reduce aprobability of air being removed with the fluid. As shown, air maycollect within the volume proximate to the top end 720 in both the mainstorage and flow path portions 730 and 732.

In the illustrated embodiment, the flexible walls 726 and 728 are bondedby heat-pressing portions of the flexible walls 726 and 728 together. Inparticular embodiments, the flexible walls 726 and 728 may beheat-pressed in a single heat-pressing step to form the partition 740,the edges 741-644, and the bag opening 736 of the reservoir bag 704.However, in alternative embodiments, the flexible walls 726 and 728 maybe held together by alternative methods, such as an adhesive or asuitable thread.

It is to be understood that the above description is intended to beillustrative, and not restrictive. For example, the above-describedembodiments (and/or aspects thereof) may be used in combination witheach other. In addition, many modifications may be made to adapt aparticular situation or material to the teachings of the inventionwithout departing from its scope. While the specific components andprocesses described herein are intended to define the parameters of thevarious embodiments of the invention, they are by no means limiting andare exemplary embodiments. Many other embodiments will be apparent tothose of skill in the art upon reviewing the above description. Thescope of the invention should, therefore, be determined with referenceto the appended claims, along with the full scope of equivalents towhich such claims are entitled. In the appended claims, the terms“including” and “in which” are used as the plain-English equivalents ofthe respective terms “comprising” and “wherein.” Moreover, in thefollowing claims, the terms “first,” “second,” and “third,” etc. areused merely as labels, and are not intended to impose numericalrequirements on their objects. Further, the limitations of the followingclaims are not written in means-plus-function format and are notintended to be interpreted based on 35 U.S.C. §112, sixth paragraph,unless and until such claim limitations expressly use the phrase “meansfor” followed by a statement of function void of further structure.

What is claimed is:
 1. (canceled)
 2. A biosensor cartridge configured toremovably engage a bioassay system, the biosensor cartridge comprising:a flow cell having inlet and outlet ports and a flow channel thatextends between the inlet and outlet ports, the flow cell including asubstrate layer and a flow cover mounted over the substrate layer withthe flow channel therebetween, the substrate layer having a substratefield in fluid communication with the flow channel, the substrate fieldincluding nucleic acids therealong for conducting a nucleic acidsequencing protocol; an activity detector secured to the flow cell toform a unitary structure, the activity detector including an array ofpixels, the substrate layer having a thickness that extends between theflow channel and the activity detector, the pixels configured to detectlight emissions that propagate through the substrate layer and areindicative of desired reactions along the substrate field; and first andsecond side surfaces, the first side surface including the inlet andoutlet ports, the second side surface comprising electrical contactsthat are communicatively coupled to the activity detector, wherein thefirst and second side surfaces face in substantially oppositedirections.
 3. The biosensor cartridge of claim 2, wherein the substratefield includes a plurality of separate reaction sites havingcorresponding nucleic acids.
 4. The biosensor cartridge of claim 3,wherein the reaction sites include recesses disposed along the substratelayer that open to the flow channel.
 5. The biosensor cartridge of claim3, wherein the reaction sites are arranged in a designated array, thecorresponding nucleic acids being immobilized to surfaces of thecorresponding reaction sites, the corresponding nucleic acids beingsequencing primers.
 6. The biosensor cartridge of claim 2, wherein thepixels are assigned to select reaction sites such that light emissionsdetected by the pixels indicate that a desired reaction has occurred atthe select reaction site, the activity detector including circuitry thatreceives and automatically associates detection signals provided by thepixels, the detection signals being representative of the lightemissions detected by the corresponding pixels from the select reactionsites.
 7. The biosensor cartridge of claim 2, wherein the pixels areassigned to select reaction sites such that light emissions detected bythe pixels indicate that a desired reaction has occurred at the selectreaction site, the activity detector including circuitry that receivesdetection signals from the pixels that are representative of the lightemissions detected by the pixels from the select reaction sites, thecircuitry configured to analyze the detection signals and generatedetection data based on the detection signals by processing thedetection signals in a designated manner.
 8. The biosensor cartridge ofclaim 2, wherein the pixels are assigned to select reaction sites suchthat light emissions detected by the pixels indicate that a desiredreaction has occurred at the select reaction site, the activity detectorincluding circuitry that receives detection signals from the pixels thatare representative of the light emissions detected by the pixels fromthe select reaction sites, the circuitry configured to automaticallymodify values of the light emissions derived from the detection signalsby weighting the values.
 9. A biosensor cartridge configured toremovably engage a bioassay system, the biosensor cartridge comprising:a flow cell including inlet and outlet ports and a flow channel thatextends therebetween, the flow cell also including a substrate field influid communication with the flow channel; an activity detector coupledto the flow cell and including an array of pixels, the pixels configuredto detect activity along the substrate field that is indicative ofdesired reactions; first and second side surfaces, the first sidesurface including the inlet and outlet ports, the second side surfacecomprising electrical contacts that are communicatively coupled to theactivity detector.
 10. The biosensor cartridge of claim 9, wherein theactivity detector comprises a microcircuit arrangement thatcommunicatively couples the pixels to the electrical contacts, themicrocircuit arrangement comprising kernels that are each associatedwith designated pixels, each kernel processing the detected activityfrom the designated pixels.
 11. The biosensor cartridge of claim 9,wherein the first side surface is shaped to engage a mating side of thebioassay system to facilitate maintaining an electrical connectionbetween the electrical contacts of the second side surface andcorresponding mating contacts of the bioassay system.
 12. The biosensorcartridge of claim 11, wherein the inlet and outlet ports are spacedapart from each other and have an engagement area extending therebetweenalong the first side surface, the engagement area being sized and shapedto engage a thermal element of the bioassay system.
 13. The biosensorcartridge of claim 9, wherein the inlet and outlet ports project awayfrom the flow channel in a common direction.
 14. The biosensor cartridgeof claim 9, wherein the first and second side surfaces face insubstantially opposite directions.
 15. The biosensor cartridge of claim9, wherein the substrate field includes a plurality of reactionchambers, the reaction chambers having apertures that open onto the flowchannel such that the reaction chambers are in fluid communication withthe flow channel.
 16. The biosensor cartridge of claim 9, wherein thepixels comprise photodetectors configured to detect light signalsgenerated along the substrate field.
 17. A method of sequencingcomprising: providing a biosensor cartridge having a flow cell includinga substrate field in fluid communication with a flow channel of the flowcell, the substrate field including a plurality of nucleic acid templatestrands located therealong, the biosensor cartridge also including anactivity detector coupled to the flow cell and including an array ofpixels, the pixels configured to detect light emissions from thesubstrate field that are indicative of desired reactions, the biosensorcartridge also having an exterior side surface that includes a pluralityof electrical contacts thereon that are communicatively coupled to thepixels; positioning the biosensor cartridge in a system receptacle of abioassay system such that the electrical contacts engage mating contactsof the bioassay system; conducting a plurality of SBS events to grow acomplementary strand by incorporating nucleotides along each templatestrand, wherein each of the plurality of SBS events includes detectingthe light emissions from the complementary strand along the substratefield, the light emissions being detected by the pixels; andcommunicating detection data to the bioassay system through theelectrical contacts, the detection data being based on the lightemissions detected by the pixels.
 18. The method of claim 17, furthercomprising fluidically coupling the inlet and outlet ports of the flowcell to respective conduits of the bioassay system, wherein conductingthe plurality of SBS events includes iteratively flowing a fluid thatincludes a mixture of different types of nucleotides.
 19. The method ofclaim 17, wherein the pixels are assigned to select reaction sites ofthe substrate field such that light emissions detected by the pixelsindicate that a desired reaction has occurred at the select reactionsite, the method further comprising analyzing detection signals from thepixels at the activity detector and generating the detection data basedon the detection signals by processing the detection signals in adesignated manner.
 20. The method of claim 17, wherein the biosensorcartridge is a self-contained, disposable unit.
 21. The method of claim17, wherein the flow channel has a flow cross-section takenperpendicular to a flow direction of the fluid, the flow cross-sectionhaving a height that changes along the flow channel to control the flowof the fluid therein.